Summary

We would like to see if there’s any interesting insights we can find through multi-omics integration approach.

library(ggfortify)
library(ggplot2)
library(dplyr)
library(factoextra)
library(pvclust)
load(file = "/Users/yetingzhang/Desktop/sema4/challenge_questions_analysis/Paper-Code-01May2018/Data/Data.Rda")
#3head(featurepatients)
featurepatients
##  [1] "PTLG002" "PTLG003" "PTLG004" "PTLG005" "PTLG007" "PTLG008" "PTLG009"
##  [8] "PTLG010" "PTLG012" "PTLG015" "PTLG016" "PTLG018" "PTLG019" "PTLG020"
## [15] "PTLG022" "PTLG024" "PTLG029" "PTLG002" "PTLG003" "PTLG004" "PTLG005"
## [22] "PTLG007" "PTLG008" "PTLG009" "PTLG010" "PTLG012" "PTLG015" "PTLG016"
## [29] "PTLG018" "PTLG019" "PTLG020" "PTLG022" "PTLG024" "PTLG029" "PTLG002"
## [36] "PTLG003" "PTLG004" "PTLG005" "PTLG007" "PTLG008" "PTLG009" "PTLG010"
## [43] "PTLG012" "PTLG015" "PTLG016" "PTLG018" "PTLG019" "PTLG020" "PTLG022"
## [50] "PTLG024" "PTLG029" "PTLG002" "PTLG003" "PTLG004" "PTLG005" "PTLG007"
## [57] "PTLG008" "PTLG009" "PTLG010" "PTLG012" "PTLG015" "PTLG016" "PTLG018"
## [64] "PTLG019" "PTLG020" "PTLG022" "PTLG024" "PTLG029"
featuretimes
## BL BL BL BL BL BL BL BL BL BL BL BL BL BL BL BL BL  1  1  1  1  1  1  1  1 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  2  2  2  2  2  2  2 
##  1  1  1  1  1  1  1  1  1  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2 
##  2  2  2  2  2  2  2  2  2  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3 
##  2  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3 
##  3  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4
#featureweeks

df <- as.data.frame(InputData[[2]]) ## plasma luminex
head(df)
##            plasma-IL17F plasma-FASL plasma-TGFA plasma-MIP1A plasma-SDF1A
## PTLG002_BL        59.00       82.00       27.75        46.00       191.25
## PTLG003_BL        87.25      221.50       48.50        71.50       186.25
## PTLG004_BL       686.50     1088.50      453.75       252.25       575.50
## PTLG005_BL        91.25      112.75       31.00        91.00       272.00
## PTLG007_BL       186.75      544.75      194.25       171.25       345.75
## PTLG008_BL        69.50      105.75       97.50        62.00       192.00
##            plasma-IL27 plasma-LIF plasma-IL1B plasma-IL2 plasma-IL4
## PTLG002_BL        70.5      35.50       28.00      31.00      56.50
## PTLG003_BL       192.5      31.00       22.00      23.50     125.50
## PTLG004_BL      1028.5     232.00       58.25     147.50     605.00
## PTLG005_BL       104.5      34.50       32.00      32.75      67.50
## PTLG007_BL       389.5      40.75       36.50      51.00     276.75
## PTLG008_BL        78.5      33.50       31.00      41.75      63.50
##            plasma-IL5 plasma-IP10 plasma-IL6 plasma-IL7 plasma-IL8
## PTLG002_BL      37.50      106.50      53.00      40.50      79.00
## PTLG003_BL      22.00      260.00     183.25      55.50     189.50
## PTLG004_BL     298.75      781.50     931.50     289.25     912.50
## PTLG005_BL      40.75      204.25      92.50      38.75     110.75
## PTLG007_BL      47.50      556.25     521.50      51.00     480.00
## PTLG008_BL      45.50      218.50      74.50      70.00     109.50
##            plasma-IL10 plasma-IFNB plasma-EOTAXIN plasma-IL12P70
## PTLG002_BL      112.00      169.00           37.5           49.5
## PTLG003_BL      160.00       67.00           53.5           78.5
## PTLG004_BL      768.75      697.00           82.0         1026.5
## PTLG005_BL      104.50       51.25           38.5           67.0
## PTLG007_BL      351.00       52.00           34.0          187.0
## PTLG008_BL      115.00       37.50           71.0           46.0
##            plasma-IL13 plasma-IL17A plasma-IL31 plasma-IL1RA plasma-SCF
## PTLG002_BL       60.00        47.50       30.50        29.50      58.50
## PTLG003_BL      151.25        48.25       51.00        24.50      79.00
## PTLG004_BL      877.00       547.50      101.00        52.00     490.00
## PTLG005_BL       94.25        49.75       30.50        31.25      59.25
## PTLG007_BL      387.00        84.50       90.75        29.50     125.75
## PTLG008_BL       63.00       106.75       39.75        31.50      57.50
##            plasma-RANTES plasma-IFNG plasma-GMCSF plasma-TNFA plasma-HGF
## PTLG002_BL       5120.00       50.50        31.00      156.50       49.5
## PTLG003_BL       4429.00      108.00       220.00      169.50       31.0
## PTLG004_BL       4850.00      449.50       392.00      243.00      104.0
## PTLG005_BL       2945.25       54.00       100.50      160.50       62.5
## PTLG007_BL       1833.50      219.25       214.25      184.00       37.5
## PTLG008_BL       3795.75       52.25        42.50      128.75       36.5
##            plasma-MIP1B plasma-IFNA plasma-TGFB plasma-MCP1 plasma-IL9
## PTLG002_BL       216.00       112.5        45.0     73.2775      52.50
## PTLG003_BL       235.25       188.5        49.0    104.0550     115.00
## PTLG004_BL       576.25       422.5       274.5    215.8500     781.00
## PTLG005_BL       187.75       102.0        48.5     81.7500      71.25
## PTLG007_BL       345.00       138.5        48.5    165.7825     380.25
## PTLG008_BL       297.50        87.0        52.5     57.5000      58.50
##            plasma-VEGFD plasma-TNFB plasma-NGF plasma-EGF plasma-BDNF
## PTLG002_BL        218.0       56.50      37.50      45.00       905.0
## PTLG003_BL         83.0      132.75      71.25     146.25       226.0
## PTLG004_BL        161.0      874.00     272.00     519.25      1009.5
## PTLG005_BL        147.5       70.25      42.50      63.50       230.0
## PTLG007_BL         76.0      365.00     138.25     145.25       447.5
## PTLG008_BL        114.5       67.00      44.00      60.50      3547.0
##            plasma-TRAIL plasma-GCSF plasma-GROA plasma-IL1A plasma-IL23
## PTLG002_BL        74.50       41.00       33.50      163.50       67.00
## PTLG003_BL        93.50       43.50       85.50      237.50      201.25
## PTLG004_BL       379.75      169.00      301.50      830.00     1072.50
## PTLG005_BL       105.00       47.25       49.50      187.25      121.75
## PTLG007_BL       221.50       82.75      180.00      449.75      591.25
## PTLG008_BL        92.25       45.00       55.25      195.00       86.75
##            plasma-IL12P40 plasma-IL15 plasma-IL18 plasma-MCSF plasma-MCP3
## PTLG002_BL         301.50        49.5      458.00       82.00       40.00
## PTLG003_BL         317.50        54.0      457.00      211.00       38.50
## PTLG004_BL         587.75       270.5     1497.50      952.75      276.00
## PTLG005_BL         216.00        45.0      368.25      125.50       48.75
## PTLG007_BL         207.25        43.5      767.25      496.50       73.00
## PTLG008_BL         246.75        46.5      404.50       83.50       41.00
##            plasma-MIG plasma-RESISTIN plasma-IL21 plasma-ICAM1
## PTLG002_BL      55.00         6791.50        35.5      1578.50
## PTLG003_BL      51.50         6377.50        34.0      1754.75
## PTLG004_BL     180.50         6057.00       126.0      2055.00
## PTLG005_BL      64.00         5574.50        48.0       812.50
## PTLG007_BL      90.00         4879.25        52.0      1764.50
## PTLG008_BL      56.75         4848.75        46.0      1650.50
##            plasma-VCAM1 plasma-FGFB plasma-IL22 plasma-PDGFBB plasma-VEGF
## PTLG002_BL     15781.00       50.50     43.0000         62.50      164.00
## PTLG003_BL     16228.25       90.00     79.6375        267.75      226.00
## PTLG004_BL     15889.00      565.50    144.7500       1145.50      845.00
## PTLG005_BL     14052.75      162.25     38.0000        256.00      222.75
## PTLG007_BL     16098.00      353.75     53.2500       1388.25      469.00
## PTLG008_BL     13638.50       59.00     52.5000        143.00      233.50
##            plasma-LEPTIN plasma-PAI1 plasma-CD40L plasma-ENA78
## PTLG002_BL        1533.5     3707.50       115.75       213.50
## PTLG003_BL        8900.5     2319.00       141.50       158.50
## PTLG004_BL        2001.5     3481.25      2731.75       724.25
## PTLG005_BL        6240.0     1768.50       120.75       178.50
## PTLG007_BL        9325.0     1855.50       176.00       301.25
## PTLG008_BL         627.0     3205.00        80.00       665.25
###quick EDA
pca_1st <- prcomp(df[18:33,])
#first_tri <- (row.names(df[17:33,]))

fviz_eig(pca_1st)

# the scree plot shows that the top 2 pcas already explained the majority of the variances in the data

# plot pc1 vs pc2 using postpartum patients microbiome dataset
fviz_pca_ind(pca_1st,
             col.ind = "cos2", # Color by the quality of representation
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
             repel = TRUE     # Avoid text overlapping
             )

## Take a look into first trimestor, as that's one of the important stage.
dis <- scale(df[18:33,], center = TRUE)
#dist_mat <- dist(dis, method = 'euclidean')
#hclust_avg <- hclust(dist_mat, method = 'average')
#plot(hclust_avg)

##use pvclust to get a confidence values
pv <- pvclust(t(dis), nboot=1000)
## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.6)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.1)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.
plot(pv, cex=0.8, cex.pv=0.7)

##G010_1, G003_1,G024_1, G002_1, G005_1 as one cluster and rest as the second cluster
df2 <- df[18:33,]
rownames(df2)
##  [1] "PTLG002_1" "PTLG003_1" "PTLG004_1" "PTLG005_1" "PTLG007_1"
##  [6] "PTLG008_1" "PTLG009_1" "PTLG010_1" "PTLG012_1" "PTLG015_1"
## [11] "PTLG016_1" "PTLG018_1" "PTLG019_1" "PTLG020_1" "PTLG022_1"
## [16] "PTLG024_1"
df2$clus <- c(1,1,0,1,0,0,0,1,0,0,0,0,0,0,0,1)

Look into the patients divided into subgroups

## we can also visualize the plasma readings for each
for (i in 1: (ncol(df2)-1)){
  hist(df2[,i], breaks = 10, main = names(df2)[i])
}

## take a look at correlation
library(corrplot)
correlations <- cor(df2)
corrplot(correlations, method="circle")

## build a logistic regression model using df2 dataframe
for (i in 1:(ncol(df2)-1)){
  test <- cor.test(df2[,i], df2$clus)
  if (test$p.value <=0.05){
    print(colnames(df2)[i])
    print(test)
  }
}
## [1] "plasma-TGFA"
## 
##  Pearson's product-moment correlation
## 
## data:  df2[, i] and df2$clus
## t = -2.5024, df = 14, p-value = 0.02535
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.8244342 -0.0831210
## sample estimates:
##        cor 
## -0.5559205 
## 
## [1] "plasma-MIP1B"
## 
##  Pearson's product-moment correlation
## 
## data:  df2[, i] and df2$clus
## t = -2.5008, df = 14, p-value = 0.02543
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.82432384 -0.08277893
## sample estimates:
##        cor 
## -0.5556824 
## 
## [1] "plasma-MCP1"
## 
##  Pearson's product-moment correlation
## 
## data:  df2[, i] and df2$clus
## t = -2.4362, df = 14, p-value = 0.0288
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.81965029 -0.06845128
## sample estimates:
##        cor 
## -0.5456421 
## 
## [1] "plasma-BDNF"
## 
##  Pearson's product-moment correlation
## 
## data:  df2[, i] and df2$clus
## t = -4.5001, df = 14, p-value = 0.0004991
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.9156315 -0.4415154
## sample estimates:
##        cor 
## -0.7689313 
## 
## [1] "plasma-VCAM1"
## 
##  Pearson's product-moment correlation
## 
## data:  df2[, i] and df2$clus
## t = 3.0593, df = 14, p-value = 0.008492
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  0.2000388 0.8591175
## sample estimates:
##       cor 
## 0.6329779
## BDNF and VCAM1 strongest signal

##head(df2)
glm.fit <- glm(clus ~ df2$`plasma-TGFA` + df2$`plasma-VCAM1` + df2$`plasma-BDNF` + df2$`plasma-MCP1` + df2$`plasma-MIP1B` , data = df2, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = clus ~ df2$`plasma-TGFA` + df2$`plasma-VCAM1` + 
##     df2$`plasma-BDNF` + df2$`plasma-MCP1` + df2$`plasma-MIP1B`, 
##     family = binomial, data = df2)
## 
## Deviance Residuals: 
##        Min          1Q      Median          3Q         Max  
## -1.499e-05  -2.110e-08  -2.110e-08   2.110e-08   1.091e-05  
## 
## Coefficients:
##                      Estimate Std. Error z value Pr(>|z|)
## (Intercept)        -4.096e+01  2.041e+06       0        1
## df2$`plasma-TGFA`   1.420e-01  1.841e+03       0        1
## df2$`plasma-VCAM1`  1.657e-02  1.273e+02       0        1
## df2$`plasma-BDNF`  -8.427e-03  1.463e+02       0        1
## df2$`plasma-MCP1`  -1.441e+00  3.693e+03       0        1
## df2$`plasma-MIP1B` -3.729e-01  3.407e+03       0        1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1.9875e+01  on 15  degrees of freedom
## Residual deviance: 5.9300e-10  on 10  degrees of freedom
## AIC: 12
## 
## Number of Fisher Scoring iterations: 25
glm.fit <- glm(clus ~ df2$`plasma-TGFA` , data = df2, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = clus ~ df2$`plasma-TGFA`, family = binomial, data = df2)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -1.13661  -0.51835  -0.06272   0.14251   1.67511  
## 
## Coefficients:
##                   Estimate Std. Error z value Pr(>|z|)
## (Intercept)        6.69565    5.16715   1.296    0.195
## df2$`plasma-TGFA` -0.08360    0.05629  -1.485    0.138
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 19.8748  on 15  degrees of freedom
## Residual deviance:  9.3253  on 14  degrees of freedom
## AIC: 13.325
## 
## Number of Fisher Scoring iterations: 8
glm.fit <- glm(clus ~ df2$`plasma-VCAM1` , data = df2, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = clus ~ df2$`plasma-VCAM1`, family = binomial, data = df2)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.6125  -0.5526  -0.2681   0.2251   1.7300  
## 
## Coefficients:
##                      Estimate Std. Error z value Pr(>|z|)  
## (Intercept)        -49.085660  26.979205  -1.819   0.0689 .
## df2$`plasma-VCAM1`   0.003295   0.001834   1.797   0.0724 .
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 19.875  on 15  degrees of freedom
## Residual deviance: 11.495  on 14  degrees of freedom
## AIC: 15.495
## 
## Number of Fisher Scoring iterations: 6
glm.fit <- glm(clus ~ df2$`plasma-BDNF` , data = df2, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = clus ~ df2$`plasma-BDNF`, family = binomial, data = df2)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -1.1587  -0.2301  -0.0766   0.1105   1.8877  
## 
## Coefficients:
##                    Estimate Std. Error z value Pr(>|z|)  
## (Intercept)        5.607621   3.617047    1.55   0.1211  
## df2$`plasma-BDNF` -0.002767   0.001618   -1.71   0.0872 .
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 19.875  on 15  degrees of freedom
## Residual deviance:  7.395  on 14  degrees of freedom
## AIC: 11.395
## 
## Number of Fisher Scoring iterations: 7
glm.fit <- glm(clus ~ df2$`plasma-MCP1` , data = df2, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = clus ~ df2$`plasma-MCP1`, family = binomial, data = df2)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -1.36285  -0.38531  -0.06863   0.23370   1.96133  
## 
## Coefficients:
##                   Estimate Std. Error z value Pr(>|z|)  
## (Intercept)       10.88083    6.25690   1.739    0.082 .
## df2$`plasma-MCP1` -0.16023    0.08875  -1.805    0.071 .
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 19.8748  on 15  degrees of freedom
## Residual deviance:  8.8399  on 14  degrees of freedom
## AIC: 12.84
## 
## Number of Fisher Scoring iterations: 7
glm.fit <- glm(clus ~ df2$`plasma-MIP1B` , data = df2, family = binomial)
summary(glm.fit)
## 
## Call:
## glm(formula = clus ~ df2$`plasma-MIP1B`, family = binomial, data = df2)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -1.39305  -0.44478  -0.09012   0.21567   1.64267  
## 
## Coefficients:
##                    Estimate Std. Error z value Pr(>|z|)  
## (Intercept)        15.69142    9.75739   1.608   0.1078  
## df2$`plasma-MIP1B` -0.06565    0.03978  -1.650   0.0989 .
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 19.875  on 15  degrees of freedom
## Residual deviance: 10.359  on 14  degrees of freedom
## AIC: 14.359
## 
## Number of Fisher Scoring iterations: 7
##BDNF strongest p-values associated with the subgroup

Use mixOmics to dig in more interesting insights

library(mixOmics)
## look into immune system
df_im <- as.data.frame(InputData[[5]]) ## immune_system
head(df_im)
##                Bcells CD16+CD56-NKcells CD4+Tcells_mem CD4+Tcells_naive
## PTLG002_BL 0.05316363       0.054978381      0.2978747       0.13628890
## PTLG003_BL 0.13733348       0.061311029      0.2742815       0.13959263
## PTLG004_BL 0.10306745       0.004127739      0.1627464       0.10394971
## PTLG005_BL 0.14980225       0.058160536      0.1418806       0.25710432
## PTLG007_BL 0.12417738       0.037422496      0.2352829       0.13274168
## PTLG008_BL 0.09616602       0.127325297      0.1960597       0.07126728
##            CD4+Tcells CD45RA+Tregs CD45RA-Tregs CD56+CD16-NKcells
## PTLG002_BL  0.4458316  0.002569880  0.013848121       0.007051946
## PTLG003_BL  0.4222384  0.004930701  0.013510121       0.004392807
## PTLG004_BL  0.2708396  0.003198210  0.007987648       0.007152648
## PTLG005_BL  0.4067580  0.013168423  0.009567682       0.002663405
## PTLG007_BL  0.3745355  0.003886490  0.008934921       0.001813028
## PTLG008_BL  0.2750212  0.002927156  0.015137576       0.007276073
##            CD7+NKcells CD8+Tcells_mem CD8+Tcells_naive CD8+Tcells
## PTLG002_BL  0.07083612     0.11888435       0.08696182  0.2085622
## PTLG003_BL  0.07506320     0.06936152       0.12489018  0.1964302
## PTLG004_BL  0.09076300     0.05706363       0.06399571  0.1216423
## PTLG005_BL  0.06900848     0.06327016       0.08158250  0.1467616
## PTLG007_BL  0.04458446     0.15057145       0.14185690  0.2980978
## PTLG008_BL  0.14730164     0.10084947       0.05528143  0.1579947
##                  cMCs        Gr      intMCs      M-MDSC        mDCs
## PTLG002_BL 0.12144206 0.7494255 0.006516047 0.004676938 0.017818647
## PTLG003_BL 0.10338336 0.5723880 0.008946982 0.002841877 0.012048841
## PTLG004_BL 0.31700093 0.7646071 0.000441132 0.005734722 0.032438990
## PTLG005_BL 0.12141926 0.6876881 0.003657895 0.040728378 0.010425002
## PTLG007_BL 0.05992007 0.4525439 0.002884818 0.009435758 0.005849769
## PTLG008_BL 0.22039690 0.7479697 0.006726484 0.037957443 0.014504355
##                  ncMCs        pDCs Tbet+CD4+Tcells_mem
## PTLG002_BL 0.026892394 0.003057061          0.05507582
## PTLG003_BL 0.006535420 0.002823947          0.05721406
## PTLG004_BL 0.000393868 0.003371512          0.04991099
## PTLG005_BL 0.011568094 0.004583800          0.01390000
## PTLG007_BL 0.003966624 0.001322208          0.04636743
## PTLG008_BL 0.017586829 0.003010789          0.03736006
##            Tbet+CD4+Tcells_naive Tbet+CD8+Tcells_mem Tbet+CD8+Tcells_naive
## PTLG002_BL           0.002082699          0.06822971            0.02619816
## PTLG003_BL           0.002752228          0.03963387            0.04932494
## PTLG004_BL           0.000850755          0.03429805            0.00436406
## PTLG005_BL           0.001337418          0.03651037            0.01527171
## PTLG007_BL           0.001171957          0.08043433            0.10015726
## PTLG008_BL           0.001433709          0.06244997            0.02283181
##            TCRgd+Tcells       Tregs Bcells_STAT1_IFNa100
## PTLG002_BL  0.008099385 0.015114792             1.883934
## PTLG003_BL  0.010417227 0.015554121             1.590320
## PTLG004_BL  0.019535866 0.009090479             1.833032
## PTLG005_BL  0.028863080 0.014197206             1.335537
## PTLG007_BL  0.009505875 0.010217062             1.097242
## PTLG008_BL  0.007192440 0.016654918             1.438130
##            CD16+CD56-NKcells_STAT1_IFNa100 CD4+Tcells_mem_STAT1_IFNa100
## PTLG002_BL                       1.3430740                     2.681511
## PTLG003_BL                       1.4153010                     2.603414
## PTLG004_BL                       1.5208184                     2.662798
## PTLG005_BL                       1.1906837                     2.240182
## PTLG007_BL                       0.8452553                     1.964598
## PTLG008_BL                       1.0641769                     2.336210
##            CD4+Tcells_naive_STAT1_IFNa100 CD4+Tcells_STAT1_IFNa100
## PTLG002_BL                       2.572645                 2.645608
## PTLG003_BL                       2.559658                 2.587365
## PTLG004_BL                       2.562652                 2.625827
## PTLG005_BL                       2.056807                 2.119978
## PTLG007_BL                       1.741210                 1.884081
## PTLG008_BL                       2.378891                 2.347843
##            CD45RA+Tregs_STAT1_IFNa100 CD45RA-Tregs_STAT1_IFNa100
## PTLG002_BL                   2.115613                   2.576695
## PTLG003_BL                   2.099454                   2.441766
## PTLG004_BL                   1.949414                   2.603367
## PTLG005_BL                   1.626340                   2.236646
## PTLG007_BL                   1.258130                   1.880639
## PTLG008_BL                   1.974352                   2.130562
##            CD56+CD16-NKcells_STAT1_IFNa100 CD7+NKcells_STAT1_IFNa100
## PTLG002_BL                        2.173771                 1.4954026
## PTLG003_BL                        1.791405                 1.4640982
## PTLG004_BL                        2.007778                 1.3896547
## PTLG005_BL                        1.685331                 1.2376270
## PTLG007_BL                        1.565739                 0.9041039
## PTLG008_BL                        1.590980                 1.0974338
##            CD8+Tcells_mem_STAT1_IFNa100 CD8+Tcells_naive_STAT1_IFNa100
## PTLG002_BL                     2.097842                       2.391814
## PTLG003_BL                     2.030723                       2.233538
## PTLG004_BL                     2.178770                       2.822410
## PTLG005_BL                     1.616216                       2.068139
## PTLG007_BL                     1.215192                       1.140393
## PTLG008_BL                     1.805588                       2.027814
##            CD8+Tcells_STAT1_IFNa100 cMCs_STAT1_IFNa100 Gr_STAT1_IFNa100
## PTLG002_BL                 2.216081           2.818281        0.9364900
## PTLG003_BL                 2.155939           3.098547        1.2513265
## PTLG004_BL                 2.513076           3.291161        0.9874188
## PTLG005_BL                 1.867359           2.552215        0.6618747
## PTLG007_BL                 1.174225           2.392938        0.7099698
## PTLG008_BL                 1.881715           2.490248        0.7945207
##            intMCs_STAT1_IFNa100 M-MDSC_STAT1_IFNa100 mDCs_STAT1_IFNa100
## PTLG002_BL             3.141909             2.559876           2.787273
## PTLG003_BL             3.239390             2.859485           2.950333
## PTLG004_BL             3.146067             3.209668           3.246538
## PTLG005_BL             2.905786             2.422720           2.450239
## PTLG007_BL             2.680093             2.303223           2.293737
## PTLG008_BL             2.541689             2.363978           2.455450
##            ncMCs_STAT1_IFNa100 pDCs_STAT1_IFNa100
## PTLG002_BL            2.529751           2.881487
## PTLG003_BL            2.558536           2.937936
## PTLG004_BL            1.549579           3.095097
## PTLG005_BL            2.442068           2.529682
## PTLG007_BL            1.760488           2.485999
## PTLG008_BL            2.160693           2.531458
##            Tbet+CD4+Tcells_mem_STAT1_IFNa100
## PTLG002_BL                          2.550036
## PTLG003_BL                          2.615164
## PTLG004_BL                          2.552131
## PTLG005_BL                          2.357239
## PTLG007_BL                          1.967606
## PTLG008_BL                          2.355129
##            Tbet+CD4+Tcells_naive_STAT1_IFNa100
## PTLG002_BL                            2.169962
## PTLG003_BL                            2.332043
## PTLG004_BL                            2.707111
## PTLG005_BL                            2.264583
## PTLG007_BL                            1.770758
## PTLG008_BL                            2.280269
##            Tbet+CD8+Tcells_mem_STAT1_IFNa100
## PTLG002_BL                         1.9350000
## PTLG003_BL                         1.9218930
## PTLG004_BL                         2.0698142
## PTLG005_BL                         1.5793980
## PTLG007_BL                         0.9484248
## PTLG008_BL                         1.7377333
##            Tbet+CD8+Tcells_naive_STAT1_IFNa100 TCRgd+Tcells_STAT1_IFNa100
## PTLG002_BL                           1.3919353                  2.0041135
## PTLG003_BL                           1.4807853                  2.0609923
## PTLG004_BL                           1.9059106                  2.0516879
## PTLG005_BL                           1.4719667                  1.5304276
## PTLG007_BL                           0.7004725                  0.9743522
## PTLG008_BL                           1.1052087                  1.6258778
##            Tregs_STAT1_IFNa100 Bcells_STAT3_IFNa100
## PTLG002_BL            2.540940             1.689828
## PTLG003_BL            2.401746             1.489384
## PTLG004_BL            2.556323             1.335289
## PTLG005_BL            2.055960             1.404200
## PTLG007_BL            1.822197             1.128299
## PTLG008_BL            2.122167             1.322829
##            CD16+CD56-NKcells_STAT3_IFNa100 CD4+Tcells_mem_STAT3_IFNa100
## PTLG002_BL                       1.4367871                     1.962873
## PTLG003_BL                       1.2032096                     1.771971
## PTLG004_BL                       1.0767724                     1.615677
## PTLG005_BL                       1.2147350                     1.740035
## PTLG007_BL                       0.8246158                     1.436556
## PTLG008_BL                       1.0578945                     1.474995
##            CD4+Tcells_naive_STAT3_IFNa100 CD4+Tcells_STAT3_IFNa100
## PTLG002_BL                       1.880874                 1.936483
## PTLG003_BL                       1.689527                 1.743107
## PTLG004_BL                       1.497626                 1.569454
## PTLG005_BL                       1.662133                 1.689146
## PTLG007_BL                       1.271081                 1.375959
## PTLG008_BL                       1.314365                 1.428821
##            CD45RA+Tregs_STAT3_IFNa100 CD45RA-Tregs_STAT3_IFNa100
## PTLG002_BL                   1.778626                   1.743283
## PTLG003_BL                   1.565153                   1.586355
## PTLG004_BL                   1.276377                   1.451046
## PTLG005_BL                   1.529707                   1.581673
## PTLG007_BL                   1.109900                   1.181956
## PTLG008_BL                   1.280025                   1.314365
##            CD56+CD16-NKcells_STAT3_IFNa100 CD7+NKcells_STAT3_IFNa100
## PTLG002_BL                        1.850616                 1.5133375
## PTLG003_BL                        1.543818                 1.2394256
## PTLG004_BL                        1.354657                 1.0545617
## PTLG005_BL                        1.634644                 1.2450130
## PTLG007_BL                        1.208692                 0.8513588
## PTLG008_BL                        1.425817                 1.0780556
##            CD8+Tcells_mem_STAT3_IFNa100 CD8+Tcells_naive_STAT3_IFNa100
## PTLG002_BL                     1.716197                      1.7909980
## PTLG003_BL                     1.501789                      1.5959655
## PTLG004_BL                     1.371408                      1.6314999
## PTLG005_BL                     1.493756                      1.6771131
## PTLG007_BL                     1.082660                      0.9755629
## PTLG008_BL                     1.429668                      1.3533569
##            CD8+Tcells_STAT3_IFNa100 cMCs_STAT3_IFNa100 Gr_STAT3_IFNa100
## PTLG002_BL                 1.745877           2.666147         1.811982
## PTLG003_BL                 1.559795           2.628044         1.866700
## PTLG004_BL                 1.507114           2.357877         1.252278
## PTLG005_BL                 1.595699           2.381356         1.480383
## PTLG007_BL                 1.028330           2.190686         1.271405
## PTLG008_BL                 1.400253           2.247682         1.351230
##            intMCs_STAT3_IFNa100 M-MDSC_STAT3_IFNa100 mDCs_STAT3_IFNa100
## PTLG002_BL             2.593384             2.653928           2.465627
## PTLG003_BL             2.500321             2.581935           2.341755
## PTLG004_BL             2.294054             2.269291           2.244720
## PTLG005_BL             2.381874             2.341738           2.160296
## PTLG007_BL             1.935910             2.172894           1.853800
## PTLG008_BL             2.026257             2.209571           2.085495
##            ncMCs_STAT3_IFNa100 pDCs_STAT3_IFNa100
## PTLG002_BL            2.202280           2.499031
## PTLG003_BL            2.108430           2.352964
## PTLG004_BL            1.417646           2.213222
## PTLG005_BL            1.999970           2.253997
## PTLG007_BL            1.415520           2.041499
## PTLG008_BL            1.732166           2.136429
##            Tbet+CD4+Tcells_mem_STAT3_IFNa100
## PTLG002_BL                          1.882823
## PTLG003_BL                          1.797875
## PTLG004_BL                          1.574886
## PTLG005_BL                          1.771802
## PTLG007_BL                          1.397375
## PTLG008_BL                          1.551601
##            Tbet+CD4+Tcells_naive_STAT3_IFNa100
## PTLG002_BL                            1.893097
## PTLG003_BL                            1.748629
## PTLG004_BL                            1.810199
## PTLG005_BL                            1.886539
## PTLG007_BL                            1.443610
## PTLG008_BL                            1.558486
##            Tbet+CD8+Tcells_mem_STAT3_IFNa100
## PTLG002_BL                         1.6250345
## PTLG003_BL                         1.4557977
## PTLG004_BL                         1.3175046
## PTLG005_BL                         1.5068274
## PTLG007_BL                         0.9126096
## PTLG008_BL                         1.4304699
##            Tbet+CD8+Tcells_naive_STAT3_IFNa100 TCRgd+Tcells_STAT3_IFNa100
## PTLG002_BL                           1.4633641                  1.6409670
## PTLG003_BL                           1.3434141                  1.5735994
## PTLG004_BL                           1.3428085                  1.3637615
## PTLG005_BL                           1.4265563                  1.5488330
## PTLG007_BL                           0.7653214                  0.9985255
## PTLG008_BL                           1.0169735                  1.4093478
##            Tregs_STAT3_IFNa100 Bcells_STAT5_IFNa100
## PTLG002_BL            1.739995            1.0865749
## PTLG003_BL            1.586866            1.0594177
## PTLG004_BL            1.454591            0.9069739
## PTLG005_BL            1.569893            0.9349606
## PTLG007_BL            1.187713            0.8141995
## PTLG008_BL            1.313346            0.9395698
##            CD16+CD56-NKcells_STAT5_IFNa100 CD4+Tcells_mem_STAT5_IFNa100
## PTLG002_BL                       0.3908686                     2.020197
## PTLG003_BL                       0.3030877                     1.826494
## PTLG004_BL                       0.3017567                     1.624617
## PTLG005_BL                       0.3224890                     1.902369
## PTLG007_BL                       0.2363487                     1.717701
## PTLG008_BL                       0.2747976                     1.790276
##            CD4+Tcells_naive_STAT5_IFNa100 CD4+Tcells_STAT5_IFNa100
## PTLG002_BL                       1.772633                 1.940625
## PTLG003_BL                       1.627500                 1.759162
## PTLG004_BL                       1.420053                 1.549337
## PTLG005_BL                       1.556633                 1.679582
## PTLG007_BL                       1.426656                 1.613615
## PTLG008_BL                       1.533184                 1.715367
##            CD45RA+Tregs_STAT5_IFNa100 CD45RA-Tregs_STAT5_IFNa100
## PTLG002_BL                   1.753596                   2.019936
## PTLG003_BL                   1.594411                   1.864885
## PTLG004_BL                   1.265761                   1.794600
## PTLG005_BL                   1.510541                   1.910700
## PTLG007_BL                   1.307160                   1.771011
## PTLG008_BL                   1.429167                   1.752876
##            CD56+CD16-NKcells_STAT5_IFNa100 CD7+NKcells_STAT5_IFNa100
## PTLG002_BL                       1.0140372                 0.5319485
## PTLG003_BL                       0.8239295                 0.3731726
## PTLG004_BL                       0.6455759                 0.3400892
## PTLG005_BL                       0.8706003                 0.3808675
## PTLG007_BL                       0.7085075                 0.3069732
## PTLG008_BL                       0.7293671                 0.3210165
##            CD8+Tcells_mem_STAT5_IFNa100 CD8+Tcells_naive_STAT5_IFNa100
## PTLG002_BL                    1.3051328                      1.4477503
## PTLG003_BL                    1.1728075                      1.1836675
## PTLG004_BL                    1.0435859                      1.3294225
## PTLG005_BL                    1.1517025                      1.3528572
## PTLG007_BL                    0.9033031                      0.6961842
## PTLG008_BL                    1.2135812                      1.1629976
##            CD8+Tcells_STAT5_IFNa100 cMCs_STAT5_IFNa100 Gr_STAT5_IFNa100
## PTLG002_BL                1.3605056           1.902063        1.0942275
## PTLG003_BL                1.1763311           2.013573        1.1997768
## PTLG004_BL                1.1905903           1.903802        0.9641738
## PTLG005_BL                1.2625255           1.628654        0.8099483
## PTLG007_BL                0.7976803           1.887401        1.0349917
## PTLG008_BL                1.1921450           1.830637        1.2142773
##            intMCs_STAT5_IFNa100 M-MDSC_STAT5_IFNa100 mDCs_STAT5_IFNa100
## PTLG002_BL             1.615392             1.893506           1.961580
## PTLG003_BL             1.667373             1.991591           2.032876
## PTLG004_BL             1.521164             1.870059           1.866350
## PTLG005_BL             1.479818             1.575791           1.784715
## PTLG007_BL             1.609355             1.858535           1.936220
## PTLG008_BL             1.532984             1.810649           1.881227
##            ncMCs_STAT5_IFNa100 pDCs_STAT5_IFNa100
## PTLG002_BL           1.3353245           1.495443
## PTLG003_BL           1.3617494           1.595920
## PTLG004_BL           0.7115761           1.588542
## PTLG005_BL           1.3103494           1.402652
## PTLG007_BL           1.0785812           1.419174
## PTLG008_BL           1.3443303           1.437497
##            Tbet+CD4+Tcells_mem_STAT5_IFNa100
## PTLG002_BL                          1.689822
## PTLG003_BL                          1.587442
## PTLG004_BL                          1.264565
## PTLG005_BL                          1.742680
## PTLG007_BL                          1.437438
## PTLG008_BL                          1.681099
##            Tbet+CD4+Tcells_naive_STAT5_IFNa100
## PTLG002_BL                            1.467632
## PTLG003_BL                            1.330122
## PTLG004_BL                            1.445521
## PTLG005_BL                            1.479403
## PTLG007_BL                            1.395989
## PTLG008_BL                            1.358936
##            Tbet+CD8+Tcells_mem_STAT5_IFNa100
## PTLG002_BL                         1.1080226
## PTLG003_BL                         0.9843562
## PTLG004_BL                         0.8832410
## PTLG005_BL                         1.0936206
## PTLG007_BL                         0.5654855
## PTLG008_BL                         1.1104924
##            Tbet+CD8+Tcells_naive_STAT5_IFNa100 TCRgd+Tcells_STAT5_IFNa100
## PTLG002_BL                           0.6882918                  1.2220701
## PTLG003_BL                           0.5877077                  1.1143876
## PTLG004_BL                           0.8312933                  0.8617033
## PTLG005_BL                           0.9551179                  1.0075779
## PTLG007_BL                           0.3231430                  0.5597269
## PTLG008_BL                           0.5339332                  1.0166648
##            Tregs_STAT5_IFNa100 Bcells_ERK_IL100
## PTLG002_BL            2.001394       0.11118083
## PTLG003_BL            1.835849       0.03854602
## PTLG004_BL            1.740703       0.07256374
## PTLG005_BL            1.797600       0.02382912
## PTLG007_BL            1.724040       0.01054052
## PTLG008_BL            1.729863      -0.02414209
##            CD16+CD56-NKcells_ERK_IL100 CD4+Tcells_mem_ERK_IL100
## PTLG002_BL                   0.5017782              0.001980188
## PTLG003_BL                   0.8162624              0.040697062
## PTLG004_BL                   1.1532978              0.087128774
## PTLG005_BL                   0.5448805              0.028279407
## PTLG007_BL                   0.8667597              0.027259055
## PTLG008_BL                   0.4821994              0.060278715
##            CD4+Tcells_naive_ERK_IL100 CD4+Tcells_ERK_IL100
## PTLG002_BL                -0.02529154         -0.006767393
## PTLG003_BL                -0.02091057          0.019518866
## PTLG004_BL                -0.01537740          0.047082156
## PTLG005_BL                 0.00398963          0.012984016
## PTLG007_BL                 0.01508464          0.022446007
## PTLG008_BL                 0.01779436          0.049181456
##            CD45RA+Tregs_ERK_IL100 CD45RA-Tregs_ERK_IL100
## PTLG002_BL             0.04076368           -0.003790391
## PTLG003_BL             0.03588799            0.036843636
## PTLG004_BL            -0.02729758           -0.029226943
## PTLG005_BL             0.01255565            0.032791105
## PTLG007_BL             0.05796270            0.056538932
## PTLG008_BL             0.03700298            0.079658894
##            CD56+CD16-NKcells_ERK_IL100 CD7+NKcells_ERK_IL100
## PTLG002_BL                    1.466490             0.6328631
## PTLG003_BL                    1.593625             0.8557783
## PTLG004_BL                    1.449741             1.0360217
## PTLG005_BL                    1.351193             0.5893691
## PTLG007_BL                    1.523448             0.8726131
## PTLG008_BL                    1.717933             0.5588017
##            CD8+Tcells_mem_ERK_IL100 CD8+Tcells_naive_ERK_IL100
## PTLG002_BL                0.2608020                0.081098431
## PTLG003_BL                0.4167038                0.167802216
## PTLG004_BL                0.4932712                0.009902669
## PTLG005_BL                0.2644027                0.023550487
## PTLG007_BL                0.3038282                0.318052197
## PTLG008_BL                0.2716617                0.092138296
##            CD8+Tcells_ERK_IL100 cMCs_ERK_IL100 Gr_ERK_IL100
## PTLG002_BL            0.1863551     0.49326507   0.08302829
## PTLG003_BL            0.2614711     0.70751505   0.14789073
## PTLG004_BL            0.2384848     1.54479760   0.49134641
## PTLG005_BL            0.1310220     0.65382322   0.09912160
## PTLG007_BL            0.3146607     0.27160103   0.21822904
## PTLG008_BL            0.2072954     0.04776473   0.06300109
##            intMCs_ERK_IL100 M-MDSC_ERK_IL100 mDCs_ERK_IL100
## PTLG002_BL        0.5812467       0.55470141     0.35095404
## PTLG003_BL        0.5598511       0.67323860     0.41838975
## PTLG004_BL        1.5286206       1.55760957     1.37329468
## PTLG005_BL        1.0215330       0.65574531     0.37064247
## PTLG007_BL        0.7576698       0.33554830     0.03053283
## PTLG008_BL        0.6033399       0.08945224     0.07272959
##            ncMCs_ERK_IL100 pDCs_ERK_IL100 Tbet+CD4+Tcells_mem_ERK_IL100
## PTLG002_BL      0.04824813     0.21963297                    0.08524395
## PTLG003_BL      0.32498934     0.16670304                    0.17616455
## PTLG004_BL      0.54095549     0.29696647                    0.22851867
## PTLG005_BL      0.46256008     0.08068998                    0.05441359
## PTLG007_BL      0.90712724     0.09960886                    0.08334648
## PTLG008_BL      0.49671749     0.20902656                    0.17136406
##            Tbet+CD4+Tcells_naive_ERK_IL100 Tbet+CD8+Tcells_mem_ERK_IL100
## PTLG002_BL                       0.2919510                     0.3204514
## PTLG003_BL                       0.2477318                     0.5920566
## PTLG004_BL                       0.5914506                     0.7120609
## PTLG005_BL                       0.3797118                     0.3478574
## PTLG007_BL                       0.4412745                     0.4516087
## PTLG008_BL                       0.3255439                     0.3609476
##            Tbet+CD8+Tcells_naive_ERK_IL100 TCRgd+Tcells_ERK_IL100
## PTLG002_BL                       0.4673205              0.3487545
## PTLG003_BL                       0.5505320              0.8193163
## PTLG004_BL                       0.6426220              1.0873612
## PTLG005_BL                       0.2361545              0.4160448
## PTLG007_BL                       0.5691801              0.7547252
## PTLG008_BL                       0.3219266              0.4296019
##            Tregs_ERK_IL100 Bcells_STAT1_IL100
## PTLG002_BL    -0.002663823          0.2395953
## PTLG003_BL     0.037917415          0.1598883
## PTLG004_BL    -0.026976770          0.2358010
## PTLG005_BL     0.011078611          0.1037533
## PTLG007_BL     0.054395346          0.1101323
## PTLG008_BL     0.075941970          0.1209797
##            CD16+CD56-NKcells_STAT1_IL100 CD4+Tcells_mem_STAT1_IL100
## PTLG002_BL                    0.16348543                  1.0305536
## PTLG003_BL                    0.20238788                  1.0315348
## PTLG004_BL                    0.37637866                  0.9169553
## PTLG005_BL                    0.09769525                  0.8139722
## PTLG007_BL                    0.11042592                  0.7439470
## PTLG008_BL                    0.07984131                  0.9087509
##            CD4+Tcells_naive_STAT1_IL100 CD4+Tcells_STAT1_IL100
## PTLG002_BL                     1.790353              1.2833408
## PTLG003_BL                     1.722792              1.2702308
## PTLG004_BL                     1.632308              1.1858182
## PTLG005_BL                     1.254344              1.0988459
## PTLG007_BL                     1.230547              0.9196233
## PTLG008_BL                     1.697326              1.1359749
##            CD45RA+Tregs_STAT1_IL100 CD45RA-Tregs_STAT1_IL100
## PTLG002_BL                1.0496766                0.9523201
## PTLG003_BL                1.0317521                0.9626436
## PTLG004_BL                0.9141909                0.9525225
## PTLG005_BL                0.7442665                0.7666832
## PTLG007_BL                0.6851043                0.8161182
## PTLG008_BL                1.0296112                0.7633486
##            CD56+CD16-NKcells_STAT1_IL100 CD7+NKcells_STAT1_IL100
## PTLG002_BL                     0.5689056               0.2240150
## PTLG003_BL                     0.5416451               0.2344680
## PTLG004_BL                     0.7370061               0.2855482
## PTLG005_BL                     0.3368075               0.1159681
## PTLG007_BL                     0.4685141               0.1368052
## PTLG008_BL                     0.4254796               0.1063011
##            CD8+Tcells_mem_STAT1_IL100 CD8+Tcells_naive_STAT1_IL100
## PTLG002_BL                  0.2837194                    1.1884136
## PTLG003_BL                  0.3655814                    0.9746334
## PTLG004_BL                  0.4263471                    1.4710208
## PTLG005_BL                  0.1499633                    0.8144214
## PTLG007_BL                  0.2124509                    0.4142098
## PTLG008_BL                  0.2054519                    0.9232063
##            CD8+Tcells_STAT1_IL100 cMCs_STAT1_IL100 Gr_STAT1_IL100
## PTLG002_BL              0.6641563        1.2479407     0.09727204
## PTLG003_BL              0.7458821        1.4790945     0.15231487
## PTLG004_BL              0.9771483        1.8594184     0.13635961
## PTLG005_BL              0.5144456        0.9411220     0.04939065
## PTLG007_BL              0.3043413        0.8895655     0.09122058
## PTLG008_BL              0.4586641        0.7200955     0.06882428
##            intMCs_STAT1_IL100 M-MDSC_STAT1_IL100 mDCs_STAT1_IL100
## PTLG002_BL          0.8345070          1.2476217        0.8862378
## PTLG003_BL          1.0594639          1.3507359        0.9880019
## PTLG004_BL          1.8313334          1.9365056        1.3272223
## PTLG005_BL          0.6694916          0.9881290        0.5363834
## PTLG007_BL          0.6907539          0.9615591        0.5832657
## PTLG008_BL          0.4427145          0.6964223        0.5289693
##            ncMCs_STAT1_IL100 pDCs_STAT1_IL100
## PTLG002_BL         0.1668810        0.6447603
## PTLG003_BL         0.2872139        0.6349425
## PTLG004_BL         0.1378978        1.1726577
## PTLG005_BL         0.1750241        0.2156090
## PTLG007_BL         0.1840795        0.4914381
## PTLG008_BL         0.1769595        0.4001473
##            Tbet+CD4+Tcells_mem_STAT1_IL100
## PTLG002_BL                       0.5956778
## PTLG003_BL                       0.6671148
## PTLG004_BL                       0.5164211
## PTLG005_BL                       0.5910468
## PTLG007_BL                       0.4859301
## PTLG008_BL                       0.6216235
##            Tbet+CD4+Tcells_naive_STAT1_IL100
## PTLG002_BL                         0.9775717
## PTLG003_BL                         0.5626643
## PTLG004_BL                         1.0831281
## PTLG005_BL                         1.1022829
## PTLG007_BL                         0.8395405
## PTLG008_BL                         1.1467345
##            Tbet+CD8+Tcells_mem_STAT1_IL100
## PTLG002_BL                       0.1966417
## PTLG003_BL                       0.2565379
## PTLG004_BL                       0.3019831
## PTLG005_BL                       0.1063076
## PTLG007_BL                       0.1019475
## PTLG008_BL                       0.1080118
##            Tbet+CD8+Tcells_naive_STAT1_IL100 TCRgd+Tcells_STAT1_IL100
## PTLG002_BL                        0.15550917               0.24980144
## PTLG003_BL                        0.15899914               0.27843610
## PTLG004_BL                        0.40468451               0.29619562
## PTLG005_BL                        0.12230364               0.12019859
## PTLG007_BL                        0.07649342               0.09983393
## PTLG008_BL                        0.08642774               0.10747571
##            Tregs_STAT1_IL100 Bcells_STAT3_IL100
## PTLG002_BL         0.9499022          0.5926661
## PTLG003_BL         0.9573398          0.3995269
## PTLG004_BL         0.9462827          0.3299872
## PTLG005_BL         0.7514386          0.3581412
## PTLG007_BL         0.8046428          0.3906252
## PTLG008_BL         0.7758609          0.4332308
##            CD16+CD56-NKcells_STAT3_IL100 CD4+Tcells_mem_STAT3_IL100
## PTLG002_BL                     0.3960812                   2.053836
## PTLG003_BL                     0.3347897                   1.908376
## PTLG004_BL                     0.4118182                   1.612510
## PTLG005_BL                     0.2460617                   2.000842
## PTLG007_BL                     0.2325240                   1.796922
## PTLG008_BL                     0.2162920                   1.657843
##            CD4+Tcells_naive_STAT3_IL100 CD4+Tcells_STAT3_IL100
## PTLG002_BL                     2.269259               2.124980
## PTLG003_BL                     2.016883               1.945915
## PTLG004_BL                     1.962275               1.742557
## PTLG005_BL                     2.182828               2.119044
## PTLG007_BL                     1.905684               1.835691
## PTLG008_BL                     1.696692               1.670309
##            CD45RA+Tregs_STAT3_IL100 CD45RA-Tregs_STAT3_IL100
## PTLG002_BL                 2.020992                 1.794446
## PTLG003_BL                 1.911368                 1.658424
## PTLG004_BL                 1.751629                 1.507646
## PTLG005_BL                 1.988284                 1.740357
## PTLG007_BL                 1.786413                 1.521907
## PTLG008_BL                 1.643127                 1.465620
##            CD56+CD16-NKcells_STAT3_IL100 CD7+NKcells_STAT3_IL100
## PTLG002_BL                     0.8822720               0.4962407
## PTLG003_BL                     0.8142312               0.3948746
## PTLG004_BL                     0.6712970               0.3404501
## PTLG005_BL                     0.6793641               0.2941397
## PTLG007_BL                     0.7013305               0.3022991
## PTLG008_BL                     0.6362252               0.2610172
##            CD8+Tcells_mem_STAT3_IL100 CD8+Tcells_naive_STAT3_IL100
## PTLG002_BL                  0.8693999                    1.8706207
## PTLG003_BL                  0.8655054                    1.4590036
## PTLG004_BL                  0.7873105                    1.9791174
## PTLG005_BL                  0.6071679                    1.8991410
## PTLG007_BL                  0.6549356                    0.8787849
## PTLG008_BL                  0.6353154                    1.3203225
##            CD8+Tcells_STAT3_IL100 cMCs_STAT3_IL100 Gr_STAT3_IL100
## PTLG002_BL              1.2886604         2.792738      0.7200121
## PTLG003_BL              1.2337297         2.703599      0.7953590
## PTLG004_BL              1.4150953         2.628698      0.2810780
## PTLG005_BL              1.3146878         2.655494      0.4798248
## PTLG007_BL              0.7528307         2.360868      0.4514897
## PTLG008_BL              0.8756156         2.165407      0.3938240
##            intMCs_STAT3_IL100 M-MDSC_STAT3_IL100 mDCs_STAT3_IL100
## PTLG002_BL           2.326279           2.842795         2.453799
## PTLG003_BL           2.319817           2.701811         2.278728
## PTLG004_BL           2.373751           2.582740         2.233316
## PTLG005_BL           2.256333           2.693906         2.054045
## PTLG007_BL           1.892205           2.420886         1.922163
## PTLG008_BL           1.443718           2.203052         1.764477
##            ncMCs_STAT3_IL100 pDCs_STAT3_IL100
## PTLG002_BL         1.3883783         2.586926
## PTLG003_BL         1.2899382         2.453399
## PTLG004_BL         0.7041160         2.478023
## PTLG005_BL         1.3540980         2.076524
## PTLG007_BL         0.8205824         2.263891
## PTLG008_BL         0.8055951         2.120495
##            Tbet+CD4+Tcells_mem_STAT3_IL100
## PTLG002_BL                        1.618937
## PTLG003_BL                        1.661021
## PTLG004_BL                        1.115886
## PTLG005_BL                        1.792288
## PTLG007_BL                        1.448666
## PTLG008_BL                        1.522800
##            Tbet+CD4+Tcells_naive_STAT3_IL100
## PTLG002_BL                          1.477918
## PTLG003_BL                          1.032364
## PTLG004_BL                          1.498180
## PTLG005_BL                          2.005625
## PTLG007_BL                          1.412778
## PTLG008_BL                          1.595287
##            Tbet+CD8+Tcells_mem_STAT3_IL100
## PTLG002_BL                       0.6271236
## PTLG003_BL                       0.6119127
## PTLG004_BL                       0.5341346
## PTLG005_BL                       0.4290052
## PTLG007_BL                       0.3207057
## PTLG008_BL                       0.3849628
##            Tbet+CD8+Tcells_naive_STAT3_IL100 TCRgd+Tcells_STAT3_IL100
## PTLG002_BL                         0.3477619                0.7144197
## PTLG003_BL                         0.3306480                0.5026466
## PTLG004_BL                         0.5434753                0.3997995
## PTLG005_BL                         0.4659108                0.3951609
## PTLG007_BL                         0.1858928                0.2505209
## PTLG008_BL                         0.1941666                0.2572802
##            Tregs_STAT3_IL100 Bcells_STAT5_IL100
## PTLG002_BL          1.803272          0.7011217
## PTLG003_BL          1.697154          0.4877259
## PTLG004_BL          1.546490          0.3559880
## PTLG005_BL          1.817593          0.4188459
## PTLG007_BL          1.562735          0.4145982
## PTLG008_BL          1.473305          0.4703189
##            CD16+CD56-NKcells_STAT5_IL100 CD4+Tcells_mem_STAT5_IL100
## PTLG002_BL                      1.714196                   2.281618
## PTLG003_BL                      1.642010                   2.170205
## PTLG004_BL                      1.635373                   2.168798
## PTLG005_BL                      1.478672                   2.237117
## PTLG007_BL                      1.598285                   2.139578
## PTLG008_BL                      1.401682                   2.140262
##            CD4+Tcells_naive_STAT5_IL100 CD4+Tcells_STAT5_IL100
## PTLG002_BL                     1.582466               2.054797
## PTLG003_BL                     1.560734               1.962617
## PTLG004_BL                     1.302549               1.847129
## PTLG005_BL                     1.581244               1.815020
## PTLG007_BL                     1.603671               1.947819
## PTLG008_BL                     1.616702               1.990917
##            CD45RA+Tregs_STAT5_IL100 CD45RA-Tregs_STAT5_IL100
## PTLG002_BL                 1.993828                 2.399908
## PTLG003_BL                 1.981066                 2.308622
## PTLG004_BL                 1.809791                 2.330400
## PTLG005_BL                 2.019320                 2.352912
## PTLG007_BL                 1.921229                 2.279483
## PTLG008_BL                 1.855102                 2.228603
##            CD56+CD16-NKcells_STAT5_IL100 CD7+NKcells_STAT5_IL100
## PTLG002_BL                      2.046668                1.755906
## PTLG003_BL                      1.859863                1.629905
## PTLG004_BL                      1.951974                1.782189
## PTLG005_BL                      1.739758                1.486918
## PTLG007_BL                      1.898545                1.593184
## PTLG008_BL                      1.775762                1.422303
##            CD8+Tcells_mem_STAT5_IL100 CD8+Tcells_naive_STAT5_IL100
## PTLG002_BL                   2.231609                     1.971236
## PTLG003_BL                   2.185057                     1.868441
## PTLG004_BL                   2.196968                     1.722882
## PTLG005_BL                   2.138116                     1.829757
## PTLG007_BL                   1.953263                     1.729812
## PTLG008_BL                   2.045576                     1.770191
##            CD8+Tcells_STAT5_IL100 cMCs_STAT5_IL100 Gr_STAT5_IL100
## PTLG002_BL               2.120877        0.8600174      0.4962128
## PTLG003_BL               1.984899        0.8563645      0.5364788
## PTLG004_BL               1.947343        0.9402423      0.4102355
## PTLG005_BL               1.967395        0.5600075      0.2558830
## PTLG007_BL               1.845892        0.7620188      0.5046695
## PTLG008_BL               1.946993        0.7711462      0.5227776
##            intMCs_STAT5_IL100 M-MDSC_STAT5_IL100 mDCs_STAT5_IL100
## PTLG002_BL          0.3469080          0.8864489        0.8689818
## PTLG003_BL          0.4784145          0.7908422        0.7970713
## PTLG004_BL          0.6665875          0.9736109        0.7550490
## PTLG005_BL          0.2222515          0.5718071        0.6025084
## PTLG007_BL          0.4347463          0.7527192        0.7894664
## PTLG008_BL          0.3955707          0.7283706        0.7883751
##            ncMCs_STAT5_IL100 pDCs_STAT5_IL100
## PTLG002_BL         0.1100864        0.2849853
## PTLG003_BL         0.1983204        0.2811485
## PTLG004_BL        -0.1232073        0.3579064
## PTLG005_BL         0.1193339        0.2418733
## PTLG007_BL         0.8275516        0.2160641
## PTLG008_BL         0.2444194        0.2205434
##            Tbet+CD4+Tcells_mem_STAT5_IL100
## PTLG002_BL                        2.345900
## PTLG003_BL                        2.299712
## PTLG004_BL                        2.217856
## PTLG005_BL                        2.291926
## PTLG007_BL                        2.154726
## PTLG008_BL                        2.267952
##            Tbet+CD4+Tcells_naive_STAT5_IL100
## PTLG002_BL                          1.854001
## PTLG003_BL                          2.137430
## PTLG004_BL                          1.652032
## PTLG005_BL                          2.008314
## PTLG007_BL                          1.972845
## PTLG008_BL                          1.869471
##            Tbet+CD8+Tcells_mem_STAT5_IL100
## PTLG002_BL                        2.206734
## PTLG003_BL                        2.220906
## PTLG004_BL                        2.203724
## PTLG005_BL                        2.166904
## PTLG007_BL                        1.863833
## PTLG008_BL                        2.051340
##            Tbet+CD8+Tcells_naive_STAT5_IL100 TCRgd+Tcells_STAT5_IL100
## PTLG002_BL                          2.094353                 2.387055
## PTLG003_BL                          1.995188                 2.313756
## PTLG004_BL                          2.002730                 2.282475
## PTLG005_BL                          2.096962                 2.179530
## PTLG007_BL                          1.734590                 1.915468
## PTLG008_BL                          1.804932                 2.087163
##            Tregs_STAT5_IL100 CD16+CD56-NKcells_CREB_LPS100
## PTLG002_BL          2.384089                   -0.20549591
## PTLG003_BL          2.279947                   -0.24007337
## PTLG004_BL          2.285439                    0.03541109
## PTLG005_BL          2.265718                   -0.19477639
## PTLG007_BL          2.260803                   -0.23369030
## PTLG008_BL          2.200156                   -0.25023098
##            CD45RA+Tregs_CREB_LPS100 CD45RA-Tregs_CREB_LPS100
## PTLG002_BL               0.14101744              -0.02258818
## PTLG003_BL              -0.02904165              -0.06543320
## PTLG004_BL               0.11152327               0.03047517
## PTLG005_BL              -0.18264177              -0.09134030
## PTLG007_BL              -0.02596627              -0.08639733
## PTLG008_BL              -0.01484645              -0.09125998
##            CD56+CD16-NKcells_CREB_LPS100 CD7+NKcells_CREB_LPS100
## PTLG002_BL                   -0.19698643             -0.20694000
## PTLG003_BL                   -0.20401176             -0.23808100
## PTLG004_BL                   -0.03997293              0.02027633
## PTLG005_BL                   -0.09335936             -0.18792888
## PTLG007_BL                   -0.17047064             -0.22249073
## PTLG008_BL                   -0.14379741             -0.23444290
##            cMCs_CREB_LPS100 Gr_CREB_LPS100 intMCs_CREB_LPS100
## PTLG002_BL       0.34311428      0.5805528          0.4987125
## PTLG003_BL       0.19051762      0.6445924          0.5591770
## PTLG004_BL       1.08836610      0.6821470          0.7478204
## PTLG005_BL       0.36612317      0.7933054          0.6840124
## PTLG007_BL       0.01994862      0.2317707          0.4824301
## PTLG008_BL       0.09295563      0.2721102          0.6550964
##            M-MDSC_CREB_LPS100 mDCs_CREB_LPS100 ncMCs_CREB_LPS100
## PTLG002_BL        0.355938946        0.4403483         0.5127153
## PTLG003_BL        0.180190575        0.1398782         0.8618568
## PTLG004_BL        1.147967408        1.2907507         0.2873403
## PTLG005_BL        0.374450213        0.4188072         0.8347602
## PTLG007_BL        0.003738333        0.0376083         0.4525493
## PTLG008_BL        0.080292173        0.1370246         0.7710514
##            Tregs_CREB_LPS100 CD16+CD56-NKcells_ERK_LPS100
## PTLG002_BL      -0.007856718                  0.016152511
## PTLG003_BL      -0.068201575                  0.010354332
## PTLG004_BL       0.050400780                  0.064435013
## PTLG005_BL      -0.122439006                  0.016047944
## PTLG007_BL      -0.081816516                  0.009141602
## PTLG008_BL      -0.088285815                  0.016829029
##            CD45RA+Tregs_ERK_LPS100 CD45RA-Tregs_ERK_LPS100
## PTLG002_BL              0.21275586             0.011584249
## PTLG003_BL              0.04996624             0.016911116
## PTLG004_BL              0.15415303             0.010625294
## PTLG005_BL              0.03451567             0.021459485
## PTLG007_BL              0.05751801             0.007061585
## PTLG008_BL              0.15036254             0.037874990
##            CD56+CD16-NKcells_ERK_LPS100 CD7+NKcells_ERK_LPS100
## PTLG002_BL                  0.013630501            0.011272548
## PTLG003_BL                 -0.007431743            0.010163186
## PTLG004_BL                  0.052309381            0.032660647
## PTLG005_BL                  0.029539137            0.017668474
## PTLG007_BL                  0.012696146            0.009381648
## PTLG008_BL                  0.018199712            0.019601785
##            cMCs_ERK_LPS100 Gr_ERK_LPS100 intMCs_ERK_LPS100
## PTLG002_BL        1.952365     0.7105355          2.357536
## PTLG003_BL        1.947608     0.6906589          2.744057
## PTLG004_BL        2.505529     0.7821723          1.793900
## PTLG005_BL        1.618730     0.5362286          2.834057
## PTLG007_BL        1.532323     0.4562182          2.454769
## PTLG008_BL        1.440713     0.3029513          2.547342
##            M-MDSC_ERK_LPS100 mDCs_ERK_LPS100 ncMCs_ERK_LPS100
## PTLG002_BL          1.545121        2.109581        2.2881374
## PTLG003_BL          1.354133        1.926142        2.6029729
## PTLG004_BL          2.299557        2.884207        0.8922558
## PTLG005_BL          1.466717        1.577241        2.3744848
## PTLG007_BL          1.319185        1.432937        1.5413898
## PTLG008_BL          1.284307        1.620961        2.3470461
##            Tregs_ERK_LPS100 CD16+CD56-NKcells_IkB_LPS100
## PTLG002_BL      0.023125687                   0.20935688
## PTLG003_BL      0.009697132                   0.09438654
## PTLG004_BL      0.032942748                  -0.03590278
## PTLG005_BL      0.006859739                   0.08113436
## PTLG007_BL      0.015756620                   0.04732308
## PTLG008_BL      0.054177064                  -0.03328707
##            CD45RA+Tregs_IkB_LPS100 CD45RA-Tregs_IkB_LPS100
## PTLG002_BL             0.147008659              0.08926275
## PTLG003_BL             0.037887028              0.06314613
## PTLG004_BL             0.034595435              0.03134623
## PTLG005_BL             0.058084646              0.04001207
## PTLG007_BL            -0.009040269             -0.02074935
## PTLG008_BL            -0.107405057             -0.07581595
##            CD56+CD16-NKcells_IkB_LPS100 CD7+NKcells_IkB_LPS100
## PTLG002_BL                 0.0087090416             0.18057942
## PTLG003_BL                 0.0007324463             0.08200923
## PTLG004_BL                 0.0809355129             0.05945091
## PTLG005_BL                 0.0083451860             0.07440806
## PTLG007_BL                 0.0170060204             0.03826008
## PTLG008_BL                -0.0396878589            -0.03546267
##            cMCs_IkB_LPS100 Gr_IkB_LPS100 intMCs_IkB_LPS100
## PTLG002_BL      -0.6440885    -0.2302899        -0.1907484
## PTLG003_BL      -0.9613265    -0.3033193        -0.5541598
## PTLG004_BL      -0.9722093    -0.3498934        -0.5976991
## PTLG005_BL      -0.5389036    -0.2655422        -0.1378193
## PTLG007_BL      -0.9801520    -0.3273486        -0.4397723
## PTLG008_BL      -1.0142779    -0.3176060        -0.5733044
##            M-MDSC_IkB_LPS100 mDCs_IkB_LPS100 ncMCs_IkB_LPS100
## PTLG002_BL        -0.4959364      -0.7385616       -0.1652233
## PTLG003_BL        -0.6746312      -0.9700044       -0.2910204
## PTLG004_BL        -0.9907348      -0.9049838       -0.4379260
## PTLG005_BL        -0.5076983      -0.7130436       -0.1044108
## PTLG007_BL        -0.8899128      -0.9619267       -0.1750182
## PTLG008_BL        -0.9750332      -0.9744760       -0.4094405
##            Tregs_IkB_LPS100 CD16+CD56-NKcells_MAPKAPK2_LPS100
## PTLG002_BL       0.09687828                        0.04511100
## PTLG003_BL       0.05556787                        0.05027454
## PTLG004_BL       0.03257948                       -0.02766143
## PTLG005_BL       0.04757067                       -0.02178715
## PTLG007_BL      -0.01041354                        0.16100935
## PTLG008_BL      -0.07330581                        0.15937056
##            CD45RA+Tregs_MAPKAPK2_LPS100 CD45RA-Tregs_MAPKAPK2_LPS100
## PTLG002_BL                  0.198207032                   0.03576117
## PTLG003_BL                  0.123005603                   0.03026736
## PTLG004_BL                  0.052514476                   0.02527546
## PTLG005_BL                  0.006451273                  -0.03447481
## PTLG007_BL                  0.199329107                   0.07715373
## PTLG008_BL                  0.228357561                   0.10363110
##            CD56+CD16-NKcells_MAPKAPK2_LPS100 CD7+NKcells_MAPKAPK2_LPS100
## PTLG002_BL                        0.06349375                 0.054902287
## PTLG003_BL                        0.07480528                 0.053145328
## PTLG004_BL                        0.01335489                 0.004631184
## PTLG005_BL                       -0.01944893                -0.016860306
## PTLG007_BL                        0.13451775                 0.149682085
## PTLG008_BL                        0.13743886                 0.152431080
##            cMCs_MAPKAPK2_LPS100 Gr_MAPKAPK2_LPS100 intMCs_MAPKAPK2_LPS100
## PTLG002_BL             1.390856          1.4384043              1.2704791
## PTLG003_BL             1.076334          1.0924306              1.1709347
## PTLG004_BL             1.493018          1.3016543              0.7069185
## PTLG005_BL             1.189113          1.0182068              1.2345900
## PTLG007_BL             1.135641          0.6403859              1.2165069
## PTLG008_BL             1.267801          0.4958583              1.2541071
##            M-MDSC_MAPKAPK2_LPS100 mDCs_MAPKAPK2_LPS100
## PTLG002_BL               1.612364            1.1631356
## PTLG003_BL               1.249096            0.8483572
## PTLG004_BL               1.614831            1.3298613
## PTLG005_BL               1.269358            0.8148355
## PTLG007_BL               1.282972            0.8139966
## PTLG008_BL               1.424968            1.0587535
##            ncMCs_MAPKAPK2_LPS100 Tregs_MAPKAPK2_LPS100
## PTLG002_BL             1.1476445            0.04973764
## PTLG003_BL             1.0967621            0.03588095
## PTLG004_BL             0.1797037            0.04180874
## PTLG005_BL             1.0737397           -0.02494619
## PTLG007_BL             0.6992199            0.09722564
## PTLG008_BL             1.2265420            0.12429454
##            CD16+CD56-NKcells_NFkB_LPS100 CD45RA+Tregs_NFkB_LPS100
## PTLG002_BL                   0.008981544              0.135162941
## PTLG003_BL                   0.013206406              0.045235854
## PTLG004_BL                   0.041123759             -0.002251015
## PTLG005_BL                   0.129511446              0.100006664
## PTLG007_BL                   0.010408951             -0.007787558
## PTLG008_BL                   0.069148952              0.097103011
##            CD45RA-Tregs_NFkB_LPS100 CD56+CD16-NKcells_NFkB_LPS100
## PTLG002_BL              0.088216413                   0.057648798
## PTLG003_BL              0.020141135                  -0.005536755
## PTLG004_BL              0.055342114                   0.032336145
## PTLG005_BL              0.107277372                   0.143304942
## PTLG007_BL             -0.026552381                  -0.035312063
## PTLG008_BL              0.004783363                   0.045399839
##            CD7+NKcells_NFkB_LPS100 cMCs_NFkB_LPS100 Gr_NFkB_LPS100
## PTLG002_BL             0.019419696        0.3648047     0.33611534
## PTLG003_BL             0.011138036        0.4213470     0.38582775
## PTLG004_BL             0.080394615        0.6894857     0.30083758
## PTLG005_BL             0.135780614        0.4507500     0.21994337
## PTLG007_BL             0.006049531        0.2994131     0.03598859
## PTLG008_BL             0.065476430        0.2972410     0.02955353
##            intMCs_NFkB_LPS100 M-MDSC_NFkB_LPS100 mDCs_NFkB_LPS100
## PTLG002_BL          0.4908122          0.3021075        0.3889814
## PTLG003_BL          0.5635687          0.3498012        0.4316558
## PTLG004_BL          0.5164665          0.6723920        0.8059898
## PTLG005_BL          0.5992361          0.4197109        0.3743859
## PTLG007_BL          0.2744813          0.2607021        0.3251304
## PTLG008_BL          0.3897066          0.2931580        0.3726967
##            ncMCs_NFkB_LPS100 Tregs_NFkB_LPS100
## PTLG002_BL        0.34094665        0.08899580
## PTLG003_BL        0.49365417        0.01698463
## PTLG004_BL        0.05811524        0.07530978
## PTLG005_BL        0.43242575        0.09756483
## PTLG007_BL        0.10831727       -0.02178815
## PTLG008_BL        0.31187626        0.01041033
##            CD16+CD56-NKcells_p38_LPS100 CD45RA+Tregs_p38_LPS100
## PTLG002_BL                   0.05785440              0.34482208
## PTLG003_BL                   0.02286360              0.09349863
## PTLG004_BL                   0.10826239              0.21527128
## PTLG005_BL                   0.03997791              0.05885838
## PTLG007_BL                  -0.02837300              0.03645351
## PTLG008_BL                  -0.04266069              0.08485487
##            CD45RA-Tregs_p38_LPS100 CD56+CD16-NKcells_p38_LPS100
## PTLG002_BL              0.08414393                 0.0687725414
## PTLG003_BL              0.05550423                -0.0008153601
## PTLG004_BL              0.18456960                 0.1031056577
## PTLG005_BL              0.03444131                 0.0483402093
## PTLG007_BL             -0.02399314                -0.0215372796
## PTLG008_BL             -0.06657235                -0.0302015580
##            CD7+NKcells_p38_LPS100 cMCs_p38_LPS100 Gr_p38_LPS100
## PTLG002_BL             0.05535226        2.339772     1.8325278
## PTLG003_BL             0.01980798        2.121308     1.5333925
## PTLG004_BL             0.13631143        3.181073     1.4790379
## PTLG005_BL             0.04279666        2.515220     1.3840292
## PTLG007_BL            -0.02389599        1.911470     0.8923686
## PTLG008_BL            -0.03817797        2.012627     0.7476081
##            intMCs_p38_LPS100 M-MDSC_p38_LPS100 mDCs_p38_LPS100
## PTLG002_BL          2.221253          2.528309        2.073169
## PTLG003_BL          2.484656          2.202611        1.640924
## PTLG004_BL          2.172893          3.343664        3.018975
## PTLG005_BL          2.700767          2.646864        1.923198
## PTLG007_BL          2.467112          2.060119        1.327613
## PTLG008_BL          2.308486          2.205805        1.702619
##            ncMCs_p38_LPS100 Tregs_p38_LPS100 CD16+CD56-NKcells_S6_LPS100
## PTLG002_BL         2.193294       0.09463160                 -0.09683664
## PTLG003_BL         2.458356       0.05061225                 -0.07219161
## PTLG004_BL         1.329431       0.20012863                 -0.15223728
## PTLG005_BL         2.492425       0.03674702                 -0.12277477
## PTLG007_BL         1.439619      -0.01842348                 -0.14723229
## PTLG008_BL         2.268346      -0.04567228                 -0.04269478
##            CD45RA+Tregs_S6_LPS100 CD45RA-Tregs_S6_LPS100
## PTLG002_BL            0.101151718           -0.030496912
## PTLG003_BL           -0.035906346           -0.028808484
## PTLG004_BL           -0.009167584            0.018029851
## PTLG005_BL           -0.054452495           -0.020934690
## PTLG007_BL           -0.017929046           -0.009322776
## PTLG008_BL            0.169234090           -0.005680856
##            CD56+CD16-NKcells_S6_LPS100 CD7+NKcells_S6_LPS100
## PTLG002_BL                -0.075554183           -0.10627246
## PTLG003_BL                -0.023323562           -0.07618660
## PTLG004_BL                -0.078897186           -0.07591937
## PTLG005_BL                -0.002650045           -0.11862976
## PTLG007_BL                -0.077534436           -0.13451729
## PTLG008_BL                -0.029806256           -0.03963849
##            cMCs_S6_LPS100 Gr_S6_LPS100 intMCs_S6_LPS100 M-MDSC_S6_LPS100
## PTLG002_BL      0.4292651   0.23223979        0.7613082        0.3682464
## PTLG003_BL      0.2273187   0.10189986        0.6070797        0.2196874
## PTLG004_BL      1.0864111   0.12479844        0.9084286        1.1694429
## PTLG005_BL      0.5082582   0.15151756        0.7968184        0.5436250
## PTLG007_BL      0.2231767   0.06822486        0.3708214        0.2601410
## PTLG008_BL      0.3051479   0.09561227        0.6837082        0.3455624
##            mDCs_S6_LPS100 ncMCs_S6_LPS100 Tregs_S6_LPS100
## PTLG002_BL      0.5152369       0.3977881    -0.017765977
## PTLG003_BL      0.2346379       0.5020941    -0.032820965
## PTLG004_BL      1.0364160       0.1701248     0.016324160
## PTLG005_BL      0.4841948       0.4370171    -0.032356324
## PTLG007_BL      0.3374240       0.1542708    -0.006793217
## PTLG008_BL      0.4051185       0.4110216     0.005905841
##            Bcells_CREB_Unstim CD16+CD56-NKcells_CREB_Unstim
## PTLG002_BL          1.3433418                      1.532027
## PTLG003_BL          0.9926098                      1.508009
## PTLG004_BL          0.7210040                      1.230525
## PTLG005_BL          1.0252745                      1.453080
## PTLG007_BL          1.2571543                      1.503886
## PTLG008_BL          1.8841074                      1.678987
##            CD4+Tcells_mem_CREB_Unstim CD4+Tcells_naive_CREB_Unstim
## PTLG002_BL                  1.1997700                    0.8457298
## PTLG003_BL                  1.1211777                    0.7980025
## PTLG004_BL                  0.9310409                    0.6724242
## PTLG005_BL                  1.1772996                    0.9531886
## PTLG007_BL                  1.1855504                    0.8468169
## PTLG008_BL                  1.1955620                    0.8363357
##            CD4+Tcells_CREB_Unstim CD45RA+Tregs_CREB_Unstim
## PTLG002_BL              1.0834691                0.9875978
## PTLG003_BL              1.0093470                0.8475886
## PTLG004_BL              0.8284817                0.6658917
## PTLG005_BL              1.0331631                0.9625428
## PTLG007_BL              1.0613300                0.8990335
## PTLG008_BL              1.0941662                0.9879212
##            CD45RA-Tregs_CREB_Unstim CD56+CD16-NKcells_CREB_Unstim
## PTLG002_BL                0.8324991                      1.324453
## PTLG003_BL                0.8222516                      1.138242
## PTLG004_BL                0.6671049                      1.031497
## PTLG005_BL                0.8571139                      1.191852
## PTLG007_BL                0.7922701                      1.240526
## PTLG008_BL                0.9377368                      1.320252
##            CD7+NKcells_CREB_Unstim CD8+Tcells_mem_CREB_Unstim
## PTLG002_BL                1.488668                   1.440155
## PTLG003_BL                1.475504                   1.319915
## PTLG004_BL                1.071216                   1.126430
## PTLG005_BL                1.428639                   1.651728
## PTLG007_BL                1.462185                   1.337312
## PTLG008_BL                1.637032                   1.691526
##            CD8+Tcells_naive_CREB_Unstim CD8+Tcells_CREB_Unstim
## PTLG002_BL                    0.9334009              1.2252535
## PTLG003_BL                    0.9386930              1.0757279
## PTLG004_BL                    0.7315596              0.9178034
## PTLG005_BL                    1.0734068              1.3281334
## PTLG007_BL                    1.1040712              1.2260894
## PTLG008_BL                    1.0715650              1.4708587
##            cMCs_CREB_Unstim Gr_CREB_Unstim intMCs_CREB_Unstim
## PTLG002_BL         2.975155       1.793294           2.977520
## PTLG003_BL         3.294566       1.781407           3.031817
## PTLG004_BL         2.229590       1.472990           2.505138
## PTLG005_BL         3.043658       1.643267           2.879241
## PTLG007_BL         3.273960       1.833146           2.871442
## PTLG008_BL         3.192141       1.689530           2.583249
##            M-MDSC_CREB_Unstim mDCs_CREB_Unstim ncMCs_CREB_Unstim
## PTLG002_BL           2.725288         2.835898          2.467263
## PTLG003_BL           3.073744         3.129188          2.297820
## PTLG004_BL           2.100119         2.012466          1.895854
## PTLG005_BL           2.952202         2.807560          2.401345
## PTLG007_BL           3.224531         3.082081          1.861059
## PTLG008_BL           3.108832         3.106337          2.156004
##            pDCs_CREB_Unstim Tbet+CD4+Tcells_mem_CREB_Unstim
## PTLG002_BL         1.454832                        1.415466
## PTLG003_BL         1.393917                        1.359145
## PTLG004_BL         1.273837                        1.126085
## PTLG005_BL         1.349529                        1.377281
## PTLG007_BL         1.605210                        1.346844
## PTLG008_BL         1.451530                        1.439356
##            Tbet+CD4+Tcells_naive_CREB_Unstim
## PTLG002_BL                          1.568470
## PTLG003_BL                          1.410527
## PTLG004_BL                          1.655602
## PTLG005_BL                          1.609416
## PTLG007_BL                          1.630289
## PTLG008_BL                          1.879834
##            Tbet+CD8+Tcells_mem_CREB_Unstim
## PTLG002_BL                        1.466800
## PTLG003_BL                        1.377181
## PTLG004_BL                        1.197759
## PTLG005_BL                        1.749744
## PTLG007_BL                        1.336534
## PTLG008_BL                        1.791499
##            Tbet+CD8+Tcells_naive_CREB_Unstim TCRgd+Tcells_CREB_Unstim
## PTLG002_BL                          1.238467                 1.742571
## PTLG003_BL                          1.228972                 1.614053
## PTLG004_BL                          1.085852                 1.328081
## PTLG005_BL                          1.585154                 1.623138
## PTLG007_BL                          1.247040                 1.395084
## PTLG008_BL                          1.393658                 1.798631
##            Tregs_CREB_Unstim Bcells_ERK_Unstim
## PTLG002_BL         0.8420510         0.2672850
## PTLG003_BL         0.8314625         0.1493333
## PTLG004_BL         0.6612819         0.1437372
## PTLG005_BL         0.8899306         0.1389144
## PTLG007_BL         0.8099278         0.1518666
## PTLG008_BL         0.9452765         0.3844152
##            CD16+CD56-NKcells_ERK_Unstim CD4+Tcells_mem_ERK_Unstim
## PTLG002_BL                    0.1980417                 0.5272692
## PTLG003_BL                    0.1400068                 0.4044905
## PTLG004_BL                    0.2062540                 0.3936610
## PTLG005_BL                    0.1342514                 0.4042180
## PTLG007_BL                    0.1228718                 0.3685582
## PTLG008_BL                    0.1564059                 0.4812678
##            CD4+Tcells_naive_ERK_Unstim CD4+Tcells_ERK_Unstim
## PTLG002_BL                   0.5836233             0.5454376
## PTLG003_BL                   0.4753995             0.4288401
## PTLG004_BL                   0.4365401             0.4112210
## PTLG005_BL                   0.4384015             0.4256636
## PTLG007_BL                   0.4062716             0.3821984
## PTLG008_BL                   0.5217830             0.4921477
##            CD45RA+Tregs_ERK_Unstim CD45RA-Tregs_ERK_Unstim
## PTLG002_BL               0.5812817               0.5692047
## PTLG003_BL               0.4554003               0.4023745
## PTLG004_BL               0.4114813               0.4435352
## PTLG005_BL               0.3950008               0.4010113
## PTLG007_BL               0.3835649               0.3528119
## PTLG008_BL               0.5329451               0.4888328
##            CD56+CD16-NKcells_ERK_Unstim CD7+NKcells_ERK_Unstim
## PTLG002_BL                    0.2074730              0.1987725
## PTLG003_BL                    0.1327644              0.1405541
## PTLG004_BL                    0.1559697              0.1454384
## PTLG005_BL                    0.1241305              0.1345663
## PTLG007_BL                    0.1342321              0.1238486
## PTLG008_BL                    0.1577764              0.1559829
##            CD8+Tcells_mem_ERK_Unstim CD8+Tcells_naive_ERK_Unstim
## PTLG002_BL                 0.4762590                   0.4914464
## PTLG003_BL                 0.3445212                   0.3714142
## PTLG004_BL                 0.3690586                   0.3897315
## PTLG005_BL                 0.3647699                   0.3923553
## PTLG007_BL                 0.3024970                   0.3077980
## PTLG008_BL                 0.4297884                   0.4428694
##            CD8+Tcells_ERK_Unstim cMCs_ERK_Unstim Gr_ERK_Unstim
## PTLG002_BL             0.4822092       1.0197033     0.5898345
## PTLG003_BL             0.3612244       1.1321097     0.5148939
## PTLG004_BL             0.3796295       0.5450609     0.3041530
## PTLG005_BL             0.3803104       0.6524384     0.2986586
## PTLG007_BL             0.3052909       1.4486824     0.5565627
## PTLG008_BL             0.4343754       1.5321937     0.4912841
##            intMCs_ERK_Unstim M-MDSC_ERK_Unstim mDCs_ERK_Unstim
## PTLG002_BL         1.3154473         0.9753772       0.6300807
## PTLG003_BL         1.1246179         1.2282288       0.5673900
## PTLG004_BL         1.0497173         0.4393444       0.4266768
## PTLG005_BL         0.6394464         0.6184404       0.3759113
## PTLG007_BL         1.3156914         1.5618929       0.7633571
## PTLG008_BL         0.8632018         1.5335981       0.9022041
##            ncMCs_ERK_Unstim pDCs_ERK_Unstim Tbet+CD4+Tcells_mem_ERK_Unstim
## PTLG002_BL        0.8102725       0.2404294                      0.5277215
## PTLG003_BL        0.6132274       0.1925976                      0.3969733
## PTLG004_BL        0.8543679       0.2220316                      0.3977953
## PTLG005_BL        0.3694352       0.1973168                      0.4111924
## PTLG007_BL        0.5666094       0.2051224                      0.3514124
## PTLG008_BL        0.3618514       0.2016478                      0.4916257
##            Tbet+CD4+Tcells_naive_ERK_Unstim Tbet+CD8+Tcells_mem_ERK_Unstim
## PTLG002_BL                        0.6447991                      0.4706652
## PTLG003_BL                        0.4658451                      0.3428644
## PTLG004_BL                        0.6809092                      0.3658209
## PTLG005_BL                        0.5367616                      0.3742293
## PTLG007_BL                        0.5120548                      0.2911482
## PTLG008_BL                        0.7494313                      0.4329718
##            Tbet+CD8+Tcells_naive_ERK_Unstim TCRgd+Tcells_ERK_Unstim
## PTLG002_BL                        0.4443277               0.6725423
## PTLG003_BL                        0.3134304               0.5029932
## PTLG004_BL                        0.3227723               0.4860715
## PTLG005_BL                        0.3568750               0.5077049
## PTLG007_BL                        0.2847943               0.3730116
## PTLG008_BL                        0.3952785               0.5810769
##            Tregs_ERK_Unstim Bcells_IkB_Unstim CD16+CD56-NKcells_IkB_Unstim
## PTLG002_BL        0.5707442         0.4957551                    0.5811274
## PTLG003_BL        0.4127159         0.6110090                    0.9202951
## PTLG004_BL        0.4370240         0.7153698                    0.9087945
## PTLG005_BL        0.4119755         0.5029687                    0.5923683
## PTLG007_BL        0.3581861         0.8040305                    1.0196055
## PTLG008_BL        0.4926159         0.4517800                    0.9258562
##            CD4+Tcells_mem_IkB_Unstim CD4+Tcells_naive_IkB_Unstim
## PTLG002_BL                 1.0146019                    1.163821
## PTLG003_BL                 1.1504247                    1.254549
## PTLG004_BL                 1.0908865                    1.162310
## PTLG005_BL                 0.8809294                    1.018979
## PTLG007_BL                 1.4665071                    1.557427
## PTLG008_BL                 1.3455708                    1.560146
##            CD4+Tcells_IkB_Unstim CD45RA+Tregs_IkB_Unstim
## PTLG002_BL             1.0633810               0.9892565
## PTLG003_BL             1.1861295               1.0765872
## PTLG004_BL             1.1192682               1.0075626
## PTLG005_BL             0.9698752               0.8199048
## PTLG007_BL             1.4991030               1.2773247
## PTLG008_BL             1.4050642               1.3772634
##            CD45RA-Tregs_IkB_Unstim CD56+CD16-NKcells_IkB_Unstim
## PTLG002_BL               0.7094038                    1.0103343
## PTLG003_BL               0.8766380                    1.1034579
## PTLG004_BL               0.8425829                    0.9517444
## PTLG005_BL               0.6440883                    0.8353730
## PTLG007_BL               1.0523057                    1.3177363
## PTLG008_BL               1.0320232                    1.1445781
##            CD7+NKcells_IkB_Unstim CD8+Tcells_mem_IkB_Unstim
## PTLG002_BL              0.6448355                 0.7923299
## PTLG003_BL              0.9328354                 0.9311403
## PTLG004_BL              0.8435762                 1.0063048
## PTLG005_BL              0.6133572                 0.8126160
## PTLG007_BL              1.0420709                 1.1496628
## PTLG008_BL              0.9392652                 1.2138526
##            CD8+Tcells_naive_IkB_Unstim CD8+Tcells_IkB_Unstim
## PTLG002_BL                    1.188597             0.9583476
## PTLG003_BL                    1.131707             1.0586876
## PTLG004_BL                    1.409275             1.2190665
## PTLG005_BL                    1.119142             0.9835524
## PTLG007_BL                    1.220997             1.1814683
## PTLG008_BL                    1.490771             1.3094550
##            cMCs_IkB_Unstim Gr_IkB_Unstim intMCs_IkB_Unstim
## PTLG002_BL       0.9492812     0.4692803         0.5001521
## PTLG003_BL       1.2997187     0.4989642         0.7791884
## PTLG004_BL       1.2388791     0.5913544         1.0760914
## PTLG005_BL       0.7735298     0.4594367         0.3034238
## PTLG007_BL       1.3727226     0.6535002         0.6138219
## PTLG008_BL       1.3057210     0.6160794         0.7690030
##            M-MDSC_IkB_Unstim mDCs_IkB_Unstim ncMCs_IkB_Unstim
## PTLG002_BL         0.7607700        1.177284        0.3031295
## PTLG003_BL         0.9426775        1.583643        0.4271982
## PTLG004_BL         1.2511315        1.191102        0.6629044
## PTLG005_BL         0.7214756        1.199609        0.2060941
## PTLG007_BL         1.2053061        1.754071        0.5821034
## PTLG008_BL         1.2089865        1.463681        0.5379507
##            pDCs_IkB_Unstim Tbet+CD4+Tcells_mem_IkB_Unstim
## PTLG002_BL        1.469599                      0.8766546
## PTLG003_BL        1.472385                      1.1094269
## PTLG004_BL        1.266636                      1.0811471
## PTLG005_BL        1.239865                      0.8679350
## PTLG007_BL        1.635122                      1.4088745
## PTLG008_BL        1.500683                      1.2728972
##            Tbet+CD4+Tcells_naive_IkB_Unstim Tbet+CD8+Tcells_mem_IkB_Unstim
## PTLG002_BL                         1.035477                      0.7079507
## PTLG003_BL                         1.166272                      0.8880699
## PTLG004_BL                         1.428714                      0.9696454
## PTLG005_BL                         1.077304                      0.8101481
## PTLG007_BL                         1.687358                      1.0083487
## PTLG008_BL                         1.714373                      1.1539838
##            Tbet+CD8+Tcells_naive_IkB_Unstim TCRgd+Tcells_IkB_Unstim
## PTLG002_BL                        0.5979821               0.7761091
## PTLG003_BL                        0.7795676               0.9839934
## PTLG004_BL                        0.9708966               1.0102838
## PTLG005_BL                        0.7988405               0.7616490
## PTLG007_BL                        0.8815053               1.0307880
## PTLG008_BL                        0.9011593               1.1006550
##            Tregs_IkB_Unstim Bcells_MAPKAPK2_Unstim
## PTLG002_BL        0.7233968               2.311810
## PTLG003_BL        0.9024052               2.596986
## PTLG004_BL        0.8572894               2.549688
## PTLG005_BL        0.7008316               2.330010
## PTLG007_BL        1.0695567               2.463802
## PTLG008_BL        1.0553373               2.433801
##            CD16+CD56-NKcells_MAPKAPK2_Unstim
## PTLG002_BL                          1.931368
## PTLG003_BL                          2.296781
## PTLG004_BL                          2.340284
## PTLG005_BL                          2.008033
## PTLG007_BL                          2.159892
## PTLG008_BL                          2.031384
##            CD4+Tcells_mem_MAPKAPK2_Unstim CD4+Tcells_naive_MAPKAPK2_Unstim
## PTLG002_BL                       2.164991                         2.177987
## PTLG003_BL                       2.417824                         2.452165
## PTLG004_BL                       2.433388                         2.456412
## PTLG005_BL                       2.268499                         2.324646
## PTLG007_BL                       2.338540                         2.433700
## PTLG008_BL                       2.259344                         2.300202
##            CD4+Tcells_MAPKAPK2_Unstim CD45RA+Tregs_MAPKAPK2_Unstim
## PTLG002_BL                   2.168045                     2.228993
## PTLG003_BL                   2.429521                     2.411254
## PTLG004_BL                   2.442567                     2.463470
## PTLG005_BL                   2.304629                     2.259092
## PTLG007_BL                   2.372634                     2.360412
## PTLG008_BL                   2.270217                     2.346650
##            CD45RA-Tregs_MAPKAPK2_Unstim CD56+CD16-NKcells_MAPKAPK2_Unstim
## PTLG002_BL                     2.019263                          2.090901
## PTLG003_BL                     2.285138                          2.397106
## PTLG004_BL                     2.351383                          2.467930
## PTLG005_BL                     2.177349                          2.200985
## PTLG007_BL                     2.224469                          2.389535
## PTLG008_BL                     2.219661                          2.157265
##            CD7+NKcells_MAPKAPK2_Unstim CD8+Tcells_mem_MAPKAPK2_Unstim
## PTLG002_BL                    1.948561                       1.927697
## PTLG003_BL                    2.293079                       2.258098
## PTLG004_BL                    2.309057                       2.300672
## PTLG005_BL                    2.018246                       2.023038
## PTLG007_BL                    2.177767                       2.118605
## PTLG008_BL                    2.040020                       2.045901
##            CD8+Tcells_naive_MAPKAPK2_Unstim CD8+Tcells_MAPKAPK2_Unstim
## PTLG002_BL                         2.101837                   1.999748
## PTLG003_BL                         2.388698                   2.340109
## PTLG004_BL                         2.468164                   2.389146
## PTLG005_BL                         2.259459                   2.154734
## PTLG007_BL                         2.211221                   2.160966
## PTLG008_BL                         2.225835                   2.109784
##            cMCs_MAPKAPK2_Unstim Gr_MAPKAPK2_Unstim intMCs_MAPKAPK2_Unstim
## PTLG002_BL             2.787907           1.465086               3.052941
## PTLG003_BL             3.277790           1.670120               3.357350
## PTLG004_BL             3.027573           1.307057               3.401704
## PTLG005_BL             2.980996           1.507802               3.167351
## PTLG007_BL             3.294925           1.577113               3.286156
## PTLG008_BL             2.999085           1.505600               2.956786
##            M-MDSC_MAPKAPK2_Unstim mDCs_MAPKAPK2_Unstim
## PTLG002_BL               2.397340             2.779791
## PTLG003_BL               2.928151             3.193225
## PTLG004_BL               2.900128             3.119748
## PTLG005_BL               2.880435             2.971891
## PTLG007_BL               3.149156             3.203224
## PTLG008_BL               2.848060             2.924449
##            ncMCs_MAPKAPK2_Unstim pDCs_MAPKAPK2_Unstim
## PTLG002_BL              2.800869             2.489211
## PTLG003_BL              3.079928             2.928867
## PTLG004_BL              2.844681             2.799909
## PTLG005_BL              2.978613             2.614913
## PTLG007_BL              2.681825             2.946109
## PTLG008_BL              2.692226             2.703571
##            Tbet+CD4+Tcells_mem_MAPKAPK2_Unstim
## PTLG002_BL                            2.192613
## PTLG003_BL                            2.447870
## PTLG004_BL                            2.437286
## PTLG005_BL                            2.390372
## PTLG007_BL                            2.306304
## PTLG008_BL                            2.297046
##            Tbet+CD4+Tcells_naive_MAPKAPK2_Unstim
## PTLG002_BL                              2.412884
## PTLG003_BL                              2.601548
## PTLG004_BL                              2.934042
## PTLG005_BL                              2.691207
## PTLG007_BL                              2.734232
## PTLG008_BL                              2.767591
##            Tbet+CD8+Tcells_mem_MAPKAPK2_Unstim
## PTLG002_BL                            1.909634
## PTLG003_BL                            2.262726
## PTLG004_BL                            2.282981
## PTLG005_BL                            2.070756
## PTLG007_BL                            2.039986
## PTLG008_BL                            2.018832
##            Tbet+CD8+Tcells_naive_MAPKAPK2_Unstim
## PTLG002_BL                              1.910503
## PTLG003_BL                              2.240830
## PTLG004_BL                              2.401180
## PTLG005_BL                              2.158052
## PTLG007_BL                              2.043273
## PTLG008_BL                              2.015452
##            TCRgd+Tcells_MAPKAPK2_Unstim Tregs_MAPKAPK2_Unstim
## PTLG002_BL                     1.984294              2.033097
## PTLG003_BL                     2.255083              2.303150
## PTLG004_BL                     2.292578              2.356123
## PTLG005_BL                     2.050059              2.211516
## PTLG007_BL                     2.219666              2.247183
## PTLG008_BL                     2.044427              2.228012
##            Bcells_NFkB_Unstim CD16+CD56-NKcells_NFkB_Unstim
## PTLG002_BL          1.4458497                     1.4910991
## PTLG003_BL          0.9206900                     1.1232214
## PTLG004_BL          0.9371759                     1.2436204
## PTLG005_BL          0.8770654                     1.0539872
## PTLG007_BL          0.7366889                     0.8596213
## PTLG008_BL          1.1750699                     1.0783717
##            CD4+Tcells_mem_NFkB_Unstim CD4+Tcells_naive_NFkB_Unstim
## PTLG002_BL                   1.632975                     1.607542
## PTLG003_BL                   1.324165                     1.261195
## PTLG004_BL                   1.380164                     1.268477
## PTLG005_BL                   1.279351                     1.206040
## PTLG007_BL                   1.220138                     1.046157
## PTLG008_BL                   1.446791                     1.307544
##            CD4+Tcells_NFkB_Unstim CD45RA+Tregs_NFkB_Unstim
## PTLG002_BL               1.623583                 1.617671
## PTLG003_BL               1.302311                 1.178572
## PTLG004_BL               1.335830                 1.230590
## PTLG005_BL               1.231706                 1.163409
## PTLG007_BL               1.155630                 1.046948
## PTLG008_BL               1.406186                 1.381399
##            CD45RA-Tregs_NFkB_Unstim CD56+CD16-NKcells_NFkB_Unstim
## PTLG002_BL                 1.638626                     1.5937663
## PTLG003_BL                 1.308981                     1.0137219
## PTLG004_BL                 1.403047                     1.2101123
## PTLG005_BL                 1.289483                     1.0405192
## PTLG007_BL                 1.197792                     0.9040109
## PTLG008_BL                 1.478304                     1.0793180
##            CD7+NKcells_NFkB_Unstim CD8+Tcells_mem_NFkB_Unstim
## PTLG002_BL               1.4926102                   1.728891
## PTLG003_BL               1.1107854                   1.326994
## PTLG004_BL               1.1684240                   1.457505
## PTLG005_BL               1.0477033                   1.435162
## PTLG007_BL               0.8588911                   1.092186
## PTLG008_BL               1.0745504                   1.461774
##            CD8+Tcells_naive_NFkB_Unstim CD8+Tcells_NFkB_Unstim
## PTLG002_BL                     1.642127               1.691105
## PTLG003_BL                     1.227144               1.261757
## PTLG004_BL                     1.337660               1.393795
## PTLG005_BL                     1.270122               1.342220
## PTLG007_BL                     1.023970               1.058992
## PTLG008_BL                     1.336478               1.416458
##            cMCs_NFkB_Unstim Gr_NFkB_Unstim intMCs_NFkB_Unstim
## PTLG002_BL         1.729852      1.2274679           1.757834
## PTLG003_BL         1.590812      1.1576161           1.596200
## PTLG004_BL         1.316812      1.2362890           1.665765
## PTLG005_BL         1.165541      0.9697881           1.248084
## PTLG007_BL         1.522954      1.2164262           1.653461
## PTLG008_BL         1.720078      1.2251825           1.594150
##            M-MDSC_NFkB_Unstim mDCs_NFkB_Unstim ncMCs_NFkB_Unstim
## PTLG002_BL           1.602751         1.515290          1.561404
## PTLG003_BL           1.504733         1.229887          1.258712
## PTLG004_BL           1.293251         1.148027          1.473683
## PTLG005_BL           1.136402         1.042600          1.111294
## PTLG007_BL           1.498294         1.110888          1.244453
## PTLG008_BL           1.661888         1.290704          1.345355
##            pDCs_NFkB_Unstim Tbet+CD4+Tcells_mem_NFkB_Unstim
## PTLG002_BL        1.1537011                        1.683029
## PTLG003_BL        0.9774160                        1.384945
## PTLG004_BL        0.9195687                        1.452596
## PTLG005_BL        0.8937160                        1.336869
## PTLG007_BL        0.9995656                        1.247298
## PTLG008_BL        1.2178527                        1.523203
##            Tbet+CD4+Tcells_naive_NFkB_Unstim
## PTLG002_BL                          1.933948
## PTLG003_BL                          1.426470
## PTLG004_BL                          1.732628
## PTLG005_BL                          1.514965
## PTLG007_BL                          1.406111
## PTLG008_BL                          1.738065
##            Tbet+CD8+Tcells_mem_NFkB_Unstim
## PTLG002_BL                        1.725984
## PTLG003_BL                        1.350625
## PTLG004_BL                        1.499026
## PTLG005_BL                        1.533150
## PTLG007_BL                        1.065169
## PTLG008_BL                        1.503976
##            Tbet+CD8+Tcells_naive_NFkB_Unstim TCRgd+Tcells_NFkB_Unstim
## PTLG002_BL                          1.616800                 2.050754
## PTLG003_BL                          1.176163                 1.571842
## PTLG004_BL                          1.404741                 1.738041
## PTLG005_BL                          1.396201                 1.551813
## PTLG007_BL                          1.013323                 1.258554
## PTLG008_BL                          1.279902                 1.548284
##            Tregs_NFkB_Unstim Bcells_p38_Unstim
## PTLG002_BL          1.635611         0.5874340
## PTLG003_BL          1.299174         0.4289286
## PTLG004_BL          1.374045         0.3860600
## PTLG005_BL          1.263957         0.3368996
## PTLG007_BL          1.183838         0.4708600
## PTLG008_BL          1.476488         0.7696062
##            CD16+CD56-NKcells_p38_Unstim CD4+Tcells_mem_p38_Unstim
## PTLG002_BL                    0.3420677                 0.3412101
## PTLG003_BL                    0.2607995                 0.2981333
## PTLG004_BL                    0.3367351                 0.2930308
## PTLG005_BL                    0.2272648                 0.2694310
## PTLG007_BL                    0.2548116                 0.3108401
## PTLG008_BL                    0.2912784                 0.3493613
##            CD4+Tcells_naive_p38_Unstim CD4+Tcells_p38_Unstim
## PTLG002_BL                   0.3219320             0.3350240
## PTLG003_BL                   0.2676521             0.2876179
## PTLG004_BL                   0.2665948             0.2826902
## PTLG005_BL                   0.2417528             0.2518099
## PTLG007_BL                   0.2799445             0.2996862
## PTLG008_BL                   0.3187144             0.3414311
##            CD45RA+Tregs_p38_Unstim CD45RA-Tregs_p38_Unstim
## PTLG002_BL               0.3580121               0.3758892
## PTLG003_BL               0.2791081               0.2774422
## PTLG004_BL               0.2296999               0.2820640
## PTLG005_BL               0.2439046               0.2635847
## PTLG007_BL               0.2900387               0.3063874
## PTLG008_BL               0.3715767               0.3743650
##            CD56+CD16-NKcells_p38_Unstim CD7+NKcells_p38_Unstim
## PTLG002_BL                    0.2888114              0.3337875
## PTLG003_BL                    0.1878317              0.2556059
## PTLG004_BL                    0.2428102              0.2646968
## PTLG005_BL                    0.1803399              0.2248029
## PTLG007_BL                    0.2049328              0.2488000
## PTLG008_BL                    0.2322562              0.2845840
##            CD8+Tcells_mem_p38_Unstim CD8+Tcells_naive_p38_Unstim
## PTLG002_BL                 0.2998695                   0.3274772
## PTLG003_BL                 0.2556867                   0.2593472
## PTLG004_BL                 0.2448911                   0.2738017
## PTLG005_BL                 0.2158268                   0.2415711
## PTLG007_BL                 0.2528654                   0.2551368
## PTLG008_BL                 0.2746403                   0.3112425
##            CD8+Tcells_p38_Unstim cMCs_p38_Unstim Gr_p38_Unstim
## PTLG002_BL             0.3114686       1.3106981     0.2618205
## PTLG003_BL             0.2575795       1.4299531     0.2273975
## PTLG004_BL             0.2598755       0.7275654     0.1644483
## PTLG005_BL             0.2304204       0.9875000     0.1974761
## PTLG007_BL             0.2539345       1.7151328     0.2236036
## PTLG008_BL             0.2877266       1.4405293     0.2471002
##            intMCs_p38_Unstim M-MDSC_p38_Unstim mDCs_p38_Unstim
## PTLG002_BL         1.4907795         1.0533968       1.2775610
## PTLG003_BL         1.2345905         1.2431856       1.4169818
## PTLG004_BL         1.1298753         0.6375527       0.7039510
## PTLG005_BL         0.9954956         0.8957083       0.9661649
## PTLG007_BL         1.2173737         1.6965473       1.5738887
## PTLG008_BL         1.0458115         1.3478662       1.3992787
##            ncMCs_p38_Unstim pDCs_p38_Unstim Tbet+CD4+Tcells_mem_p38_Unstim
## PTLG002_BL        1.3702681       0.5983727                      0.3489453
## PTLG003_BL        1.0195736       0.5934122                      0.3037197
## PTLG004_BL        0.8428859       0.4164223                      0.2762782
## PTLG005_BL        0.8943996       0.5100921                      0.2961469
## PTLG007_BL        0.7389302       0.5509278                      0.2960594
## PTLG008_BL        0.8613081       0.5618226                      0.3667232
##            Tbet+CD4+Tcells_naive_p38_Unstim Tbet+CD8+Tcells_mem_p38_Unstim
## PTLG002_BL                        0.5635131                      0.3182769
## PTLG003_BL                        0.3765790                      0.2588440
## PTLG004_BL                        0.6528826                      0.2408653
## PTLG005_BL                        0.3980845                      0.2125897
## PTLG007_BL                        0.5366995                      0.2545642
## PTLG008_BL                        0.6564478                      0.2707079
##            Tbet+CD8+Tcells_naive_p38_Unstim TCRgd+Tcells_p38_Unstim
## PTLG002_BL                        0.3249345               0.3734880
## PTLG003_BL                        0.2570437               0.2671310
## PTLG004_BL                        0.2723772               0.2230888
## PTLG005_BL                        0.2315289               0.2098211
## PTLG007_BL                        0.2482516               0.3109623
## PTLG008_BL                        0.3096221               0.2574379
##            Tregs_p38_Unstim Bcells_S6_Unstim CD16+CD56-NKcells_S6_Unstim
## PTLG002_BL        0.3784539         1.930306                   1.0734334
## PTLG003_BL        0.2793828         1.878084                   1.0721098
## PTLG004_BL        0.2747268         1.670232                   1.0398857
## PTLG005_BL        0.2625646         1.834203                   0.8787435
## PTLG007_BL        0.3080039         1.849743                   1.0491883
## PTLG008_BL        0.3749344         1.876035                   0.9557624
##            CD4+Tcells_mem_S6_Unstim CD4+Tcells_naive_S6_Unstim
## PTLG002_BL                0.4016325                  0.6457943
## PTLG003_BL                0.3255893                  0.6400155
## PTLG004_BL                0.2344455                  0.7725610
## PTLG005_BL                0.3521391                  0.6572289
## PTLG007_BL                0.3012091                  0.7160773
## PTLG008_BL                0.3359148                  0.5692703
##            CD4+Tcells_S6_Unstim CD45RA+Tregs_S6_Unstim
## PTLG002_BL            0.4760231              0.6224378
## PTLG003_BL            0.4293711              0.5877025
## PTLG004_BL            0.4409139              0.5919307
## PTLG005_BL            0.5450173              0.5867731
## PTLG007_BL            0.4482957              0.5597560
## PTLG008_BL            0.3963204              0.5419513
##            CD45RA-Tregs_S6_Unstim CD56+CD16-NKcells_S6_Unstim
## PTLG002_BL              0.3359727                   0.6744689
## PTLG003_BL              0.2830967                   0.7231868
## PTLG004_BL              0.2076796                   0.8419811
## PTLG005_BL              0.2926156                   0.6947684
## PTLG007_BL              0.2386271                   0.7462732
## PTLG008_BL              0.3286172                   0.5272477
##            CD7+NKcells_S6_Unstim CD8+Tcells_mem_S6_Unstim
## PTLG002_BL             1.0042266                0.5065821
## PTLG003_BL             1.0492967                0.4086545
## PTLG004_BL             0.8721581                0.2980804
## PTLG005_BL             0.8692915                0.5571489
## PTLG007_BL             1.0182885                0.3931909
## PTLG008_BL             0.9178381                0.5024024
##            CD8+Tcells_naive_S6_Unstim CD8+Tcells_S6_Unstim cMCs_S6_Unstim
## PTLG002_BL                  0.9850361            0.7062456      1.4882139
## PTLG003_BL                  1.0900121            0.8422466      1.6479710
## PTLG004_BL                  1.2410788            0.7944779      0.5753761
## PTLG005_BL                  0.9736546            0.7893189      1.1647444
## PTLG007_BL                  1.1460575            0.7536819      1.4702866
## PTLG008_BL                  0.9178029            0.6478817      1.4457350
##            Gr_S6_Unstim intMCs_S6_Unstim M-MDSC_S6_Unstim mDCs_S6_Unstim
## PTLG002_BL    0.7150361        1.3681202        1.2402753      1.2937126
## PTLG003_BL    0.8055508        1.3505985        1.3747832      1.3956525
## PTLG004_BL    0.5250316        0.9135330        0.4351164      0.5455454
## PTLG005_BL    0.5253063        0.9859561        1.0483856      1.0132584
## PTLG007_BL    0.6223058        1.2265534        1.3184417      1.0041317
## PTLG008_BL    0.5132232        0.9306923        1.2505613      1.1954048
##            ncMCs_S6_Unstim pDCs_S6_Unstim Tbet+CD4+Tcells_mem_S6_Unstim
## PTLG002_BL       1.1149569      0.9473491                     0.4723082
## PTLG003_BL       1.0009342      0.9254935                     0.3960724
## PTLG004_BL       0.7919038      0.8040769                     0.2775185
## PTLG005_BL       0.8984885      0.8005398                     0.4100194
## PTLG007_BL       1.0303611      0.9492261                     0.3506848
## PTLG008_BL       0.7430516      0.8140353                     0.3986797
##            Tbet+CD4+Tcells_naive_S6_Unstim Tbet+CD8+Tcells_mem_S6_Unstim
## PTLG002_BL                       1.0575421                     0.5086470
## PTLG003_BL                       0.7881706                     0.4265873
## PTLG004_BL                       1.0953875                     0.3201406
## PTLG005_BL                       0.8850472                     0.5994524
## PTLG007_BL                       0.8997395                     0.3972660
## PTLG008_BL                       0.9322777                     0.5478698
##            Tbet+CD8+Tcells_naive_S6_Unstim TCRgd+Tcells_S6_Unstim
## PTLG002_BL                       0.8301758              0.7412374
## PTLG003_BL                       0.9519362              0.5948369
## PTLG004_BL                       0.6492401              0.3701913
## PTLG005_BL                       0.7355286              0.5924967
## PTLG007_BL                       0.9237288              1.0957695
## PTLG008_BL                       0.7574023              0.5262540
##            Tregs_S6_Unstim Bcells_STAT1_Unstim
## PTLG002_BL       0.3517799           0.2173282
## PTLG003_BL       0.3132209           0.1653385
## PTLG004_BL       0.2375856           0.1756185
## PTLG005_BL       0.3882727           0.1333492
## PTLG007_BL       0.2724968           0.1555878
## PTLG008_BL       0.3452982           0.2389696
##            CD16+CD56-NKcells_STAT1_Unstim CD4+Tcells_mem_STAT1_Unstim
## PTLG002_BL                      0.1601705                   0.1682887
## PTLG003_BL                      0.1751036                   0.1719418
## PTLG004_BL                      0.2112317                   0.1953503
## PTLG005_BL                      0.1441915                   0.1509593
## PTLG007_BL                      0.1543973                   0.1680713
## PTLG008_BL                      0.1859641                   0.2053465
##            CD4+Tcells_naive_STAT1_Unstim CD4+Tcells_STAT1_Unstim
## PTLG002_BL                     0.1620959               0.1662434
## PTLG003_BL                     0.1651676               0.1697243
## PTLG004_BL                     0.1913301               0.1935840
## PTLG005_BL                     0.1301516               0.1375446
## PTLG007_BL                     0.1559919               0.1637041
## PTLG008_BL                     0.2075118               0.2059915
##            CD45RA+Tregs_STAT1_Unstim CD45RA-Tregs_STAT1_Unstim
## PTLG002_BL                 0.2131215                 0.1636117
## PTLG003_BL                 0.1563510                 0.1579927
## PTLG004_BL                 0.1852947                 0.1914989
## PTLG005_BL                 0.1233058                 0.1452268
## PTLG007_BL                 0.1574041                 0.1564620
## PTLG008_BL                 0.2182978                 0.2113028
##            CD56+CD16-NKcells_STAT1_Unstim CD7+NKcells_STAT1_Unstim
## PTLG002_BL                      0.1651819                0.1609661
## PTLG003_BL                      0.1295451                0.1698291
## PTLG004_BL                      0.1815409                0.1763395
## PTLG005_BL                      0.1086348                0.1410629
## PTLG007_BL                      0.1423653                0.1515970
## PTLG008_BL                      0.1691002                0.1829980
##            CD8+Tcells_mem_STAT1_Unstim CD8+Tcells_naive_STAT1_Unstim
## PTLG002_BL                   0.1488153                     0.1607185
## PTLG003_BL                   0.1540996                     0.1624510
## PTLG004_BL                   0.1720980                     0.1966202
## PTLG005_BL                   0.1225920                     0.1342914
## PTLG007_BL                   0.1453974                     0.1430933
## PTLG008_BL                   0.1611283                     0.1891478
##            CD8+Tcells_STAT1_Unstim cMCs_STAT1_Unstim Gr_STAT1_Unstim
## PTLG002_BL               0.1538079         0.5444915       0.2674106
## PTLG003_BL               0.1592279         0.6028097       0.2547346
## PTLG004_BL               0.1848295         0.5789640       0.2517249
## PTLG005_BL               0.1288318         0.4001107       0.2129104
## PTLG007_BL               0.1440179         0.6298806       0.2157086
## PTLG008_BL               0.1709610         0.5880563       0.2097999
##            intMCs_STAT1_Unstim M-MDSC_STAT1_Unstim mDCs_STAT1_Unstim
## PTLG002_BL           0.7310422           0.4652058         0.4800233
## PTLG003_BL           0.7194218           0.5057740         0.5243222
## PTLG004_BL           0.7216133           0.5173512         0.5769989
## PTLG005_BL           0.5026929           0.3732078         0.3582773
## PTLG007_BL           0.6619458           0.6162480         0.4673856
## PTLG008_BL           0.6092257           0.5492420         0.5020325
##            ncMCs_STAT1_Unstim pDCs_STAT1_Unstim
## PTLG002_BL          0.6700006         0.2745749
## PTLG003_BL          0.6345784         0.2836829
## PTLG004_BL          0.6893175         0.2705679
## PTLG005_BL          0.4334836         0.2574702
## PTLG007_BL          0.4038871         0.2868132
## PTLG008_BL          0.5209884         0.3068360
##            Tbet+CD4+Tcells_mem_STAT1_Unstim
## PTLG002_BL                        0.1751050
## PTLG003_BL                        0.1718114
## PTLG004_BL                        0.1818860
## PTLG005_BL                        0.1671244
## PTLG007_BL                        0.1647998
## PTLG008_BL                        0.2131390
##            Tbet+CD4+Tcells_naive_STAT1_Unstim
## PTLG002_BL                          0.3208015
## PTLG003_BL                          0.1950628
## PTLG004_BL                          0.5381641
## PTLG005_BL                          0.2736873
## PTLG007_BL                          0.3466748
## PTLG008_BL                          0.4251483
##            Tbet+CD8+Tcells_mem_STAT1_Unstim
## PTLG002_BL                        0.1540192
## PTLG003_BL                        0.1511497
## PTLG004_BL                        0.1645606
## PTLG005_BL                        0.1232316
## PTLG007_BL                        0.1441921
## PTLG008_BL                        0.1579541
##            Tbet+CD8+Tcells_naive_STAT1_Unstim TCRgd+Tcells_STAT1_Unstim
## PTLG002_BL                          0.1484545                 0.1608881
## PTLG003_BL                          0.1546765                 0.1498558
## PTLG004_BL                          0.1765572                 0.1661662
## PTLG005_BL                          0.1396455                 0.1348518
## PTLG007_BL                          0.1366142                 0.1861696
## PTLG008_BL                          0.1768606                 0.1708635
##            Tregs_STAT1_Unstim Bcells_STAT3_Unstim
## PTLG002_BL          0.1662114           0.2781483
## PTLG003_BL          0.1603167           0.1625053
## PTLG004_BL          0.1873261           0.1718254
## PTLG005_BL          0.1455273           0.2120853
## PTLG007_BL          0.1562396           0.1630811
## PTLG008_BL          0.2135246           0.2225361
##            CD16+CD56-NKcells_STAT3_Unstim CD4+Tcells_mem_STAT3_Unstim
## PTLG002_BL                      0.2218000                   0.2845663
## PTLG003_BL                      0.1571439                   0.3237056
## PTLG004_BL                      0.2041983                   0.2849812
## PTLG005_BL                      0.1995070                   0.3620370
## PTLG007_BL                      0.1603064                   0.3329184
## PTLG008_BL                      0.1545146                   0.4297146
##            CD4+Tcells_naive_STAT3_Unstim CD4+Tcells_STAT3_Unstim
## PTLG002_BL                     0.3356009               0.3013098
## PTLG003_BL                     0.4034801               0.3510125
## PTLG004_BL                     0.3652782               0.3170946
## PTLG005_BL                     0.3678771               0.3662373
## PTLG007_BL                     0.4285801               0.3684858
## PTLG008_BL                     0.6534357               0.4939236
##            CD45RA+Tregs_STAT3_Unstim CD45RA-Tregs_STAT3_Unstim
## PTLG002_BL                 0.3864844                 0.2641090
## PTLG003_BL                 0.3128324                 0.2692223
## PTLG004_BL                 0.3045837                 0.2497949
## PTLG005_BL                 0.3038926                 0.3106597
## PTLG007_BL                 0.3211479                 0.3014530
## PTLG008_BL                 0.5114759                 0.3606454
##            CD56+CD16-NKcells_STAT3_Unstim CD7+NKcells_STAT3_Unstim
## PTLG002_BL                      0.2393239                0.2211650
## PTLG003_BL                      0.1389597                0.1560172
## PTLG004_BL                      0.1505888                0.1668143
## PTLG005_BL                      0.2045774                0.1993931
## PTLG007_BL                      0.1732497                0.1599824
## PTLG008_BL                      0.1504352                0.1531552
##            CD8+Tcells_mem_STAT3_Unstim CD8+Tcells_naive_STAT3_Unstim
## PTLG002_BL                   0.2178882                     0.2709459
## PTLG003_BL                   0.1745433                     0.2512281
## PTLG004_BL                   0.1887592                     0.2843483
## PTLG005_BL                   0.2065138                     0.2840917
## PTLG007_BL                   0.1838739                     0.2202050
## PTLG008_BL                   0.1843703                     0.3486748
##            CD8+Tcells_STAT3_Unstim cMCs_STAT3_Unstim Gr_STAT3_Unstim
## PTLG002_BL               0.2398396         0.5552704       0.5746168
## PTLG003_BL               0.2233878         0.5329927       0.5871720
## PTLG004_BL               0.2388598         0.7365765       0.7397921
## PTLG005_BL               0.2497757         0.6053640       0.6618063
## PTLG007_BL               0.2005771         0.6242293       0.7589489
## PTLG008_BL               0.2424071         0.5838936       0.7142144
##            intMCs_STAT3_Unstim M-MDSC_STAT3_Unstim mDCs_STAT3_Unstim
## PTLG002_BL           0.5952397           0.5391052         0.5493400
## PTLG003_BL           0.5040039           0.5216607         0.5967189
## PTLG004_BL           0.8677943           0.8552758         0.5897723
## PTLG005_BL           0.5062227           0.6450598         0.5820798
## PTLG007_BL           0.5238370           0.6732392         0.6832180
## PTLG008_BL           0.4805024           0.6178903         0.5726557
##            ncMCs_STAT3_Unstim pDCs_STAT3_Unstim
## PTLG002_BL          0.4942574         0.3503243
## PTLG003_BL          0.3897859         0.3328578
## PTLG004_BL          0.6645261         0.2903678
## PTLG005_BL          0.4454081         0.3886589
## PTLG007_BL          0.2812737         0.3587549
## PTLG008_BL          0.3594660         0.3556967
##            Tbet+CD4+Tcells_mem_STAT3_Unstim
## PTLG002_BL                        0.2493262
## PTLG003_BL                        0.2266845
## PTLG004_BL                        0.2142891
## PTLG005_BL                        0.3131146
## PTLG007_BL                        0.2320790
## PTLG008_BL                        0.3097553
##            Tbet+CD4+Tcells_naive_STAT3_Unstim
## PTLG002_BL                          0.4818524
## PTLG003_BL                          0.2904628
## PTLG004_BL                          0.5536225
## PTLG005_BL                          0.5261899
## PTLG007_BL                          0.4896744
## PTLG008_BL                          0.6811571
##            Tbet+CD8+Tcells_mem_STAT3_Unstim
## PTLG002_BL                        0.2189375
## PTLG003_BL                        0.1578626
## PTLG004_BL                        0.1709310
## PTLG005_BL                        0.2022413
## PTLG007_BL                        0.1639236
## PTLG008_BL                        0.1678895
##            Tbet+CD8+Tcells_naive_STAT3_Unstim TCRgd+Tcells_STAT3_Unstim
## PTLG002_BL                          0.2218408                 0.2519930
## PTLG003_BL                          0.1634312                 0.1816717
## PTLG004_BL                          0.2064093                 0.1901294
## PTLG005_BL                          0.2201852                 0.2324579
## PTLG007_BL                          0.1588787                 0.1895293
## PTLG008_BL                          0.1721998                 0.1742372
##            Tregs_STAT3_Unstim Bcells_STAT5_Unstim
## PTLG002_BL          0.2749372           0.5080754
## PTLG003_BL          0.2696643           0.2746148
## PTLG004_BL          0.2489255           0.2753367
## PTLG005_BL          0.3107475           0.3198885
## PTLG007_BL          0.3027992           0.2222449
## PTLG008_BL          0.3672610           0.3596088
##            CD16+CD56-NKcells_STAT5_Unstim CD4+Tcells_mem_STAT5_Unstim
## PTLG002_BL                      0.4370299                   0.5188143
## PTLG003_BL                      0.3536102                   0.4791554
## PTLG004_BL                      0.4106613                   0.4925632
## PTLG005_BL                      0.3824558                   0.4873415
## PTLG007_BL                      0.3033436                   0.4470768
## PTLG008_BL                      0.3591477                   0.5123885
##            CD4+Tcells_naive_STAT5_Unstim CD4+Tcells_STAT5_Unstim
## PTLG002_BL                     0.5319969               0.5231944
## PTLG003_BL                     0.4937010               0.4840921
## PTLG004_BL                     0.5093203               0.4989418
## PTLG005_BL                     0.4657778               0.4737736
## PTLG007_BL                     0.4565514               0.4503689
## PTLG008_BL                     0.5411095               0.5213035
##            CD45RA+Tregs_STAT5_Unstim CD45RA-Tregs_STAT5_Unstim
## PTLG002_BL                 0.6418038                 0.5244315
## PTLG003_BL                 0.4078199                 0.3828482
## PTLG004_BL                 0.4698334                 0.4342122
## PTLG005_BL                 0.4109841                 0.4190715
## PTLG007_BL                 0.3458056                 0.3345147
## PTLG008_BL                 0.5153179                 0.4317007
##            CD56+CD16-NKcells_STAT5_Unstim CD7+NKcells_STAT5_Unstim
## PTLG002_BL                      0.4594220                0.4393125
## PTLG003_BL                      0.3274354                0.3529796
## PTLG004_BL                      0.3978362                0.3660071
## PTLG005_BL                      0.4254497                0.3882079
## PTLG007_BL                      0.3374606                0.2994207
## PTLG008_BL                      0.3564407                0.3531437
##            CD8+Tcells_mem_STAT5_Unstim CD8+Tcells_naive_STAT5_Unstim
## PTLG002_BL                   0.4664585                     0.5471628
## PTLG003_BL                   0.3849776                     0.4295466
## PTLG004_BL                   0.3966512                     0.5437557
## PTLG005_BL                   0.4105237                     0.5067977
## PTLG007_BL                   0.3487510                     0.3753280
## PTLG008_BL                   0.4020581                     0.4785952
##            CD8+Tcells_STAT5_Unstim cMCs_STAT5_Unstim Gr_STAT5_Unstim
## PTLG002_BL               0.5003172         1.0997438       0.7654855
## PTLG003_BL               0.4134202         1.0024210       0.5889620
## PTLG004_BL               0.4741971         0.8906038       0.4764761
## PTLG005_BL               0.4639764         0.9922790       0.6257502
## PTLG007_BL               0.3609189         0.8873429       0.5034246
## PTLG008_BL               0.4290462         0.8757932       0.4601436
##            intMCs_STAT5_Unstim M-MDSC_STAT5_Unstim mDCs_STAT5_Unstim
## PTLG002_BL           1.3269441           0.9989541         0.9536371
## PTLG003_BL           1.1261494           0.9448678         0.8219467
## PTLG004_BL           1.2176661           0.8904046         0.8004679
## PTLG005_BL           1.0980149           0.9935417         0.7914198
## PTLG007_BL           0.9748642           0.9058031         0.6493813
## PTLG008_BL           0.9085742           0.8440518         0.7590346
##            ncMCs_STAT5_Unstim pDCs_STAT5_Unstim
## PTLG002_BL          1.0826295         0.8086104
## PTLG003_BL          0.9074171         0.6042555
## PTLG004_BL          1.0677888         0.5636154
## PTLG005_BL          0.8695965         0.6801389
## PTLG007_BL          0.5646013         0.5480772
## PTLG008_BL          0.7263003         0.5794442
##            Tbet+CD4+Tcells_mem_STAT5_Unstim
## PTLG002_BL                        0.5042688
## PTLG003_BL                        0.4494896
## PTLG004_BL                        0.4645632
## PTLG005_BL                        0.5063484
## PTLG007_BL                        0.3938714
## PTLG008_BL                        0.4756519
##            Tbet+CD4+Tcells_naive_STAT5_Unstim
## PTLG002_BL                          0.7574242
## PTLG003_BL                          0.4938482
## PTLG004_BL                          1.0044966
## PTLG005_BL                          0.7539782
## PTLG007_BL                          0.6493930
## PTLG008_BL                          0.8755706
##            Tbet+CD8+Tcells_mem_STAT5_Unstim
## PTLG002_BL                        0.4620451
## PTLG003_BL                        0.3694388
## PTLG004_BL                        0.3785570
## PTLG005_BL                        0.4029049
## PTLG007_BL                        0.3210094
## PTLG008_BL                        0.3816272
##            Tbet+CD8+Tcells_naive_STAT5_Unstim TCRgd+Tcells_STAT5_Unstim
## PTLG002_BL                          0.4546654                 0.4438595
## PTLG003_BL                          0.3524330                 0.3120759
## PTLG004_BL                          0.4235297                 0.3323679
## PTLG005_BL                          0.4344997                 0.3718802
## PTLG007_BL                          0.3003717                 0.2974487
## PTLG008_BL                          0.3565438                 0.3283151
##            Tregs_STAT5_Unstim
## PTLG002_BL          0.5294306
## PTLG003_BL          0.3885832
## PTLG004_BL          0.4479044
## PTLG005_BL          0.4218850
## PTLG007_BL          0.3328335
## PTLG008_BL          0.4391577
dis_im <- scale(df_im[18:33,], center = TRUE)

##use pvclust to get a confidence values
pv_im <- pvclust(t(dis_im), nboot=1000)
## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.6)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.1)... Done.
## Bootstrap (r = 1.2)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.4)... Done.
plot(pv_im, cex=0.8, cex.pv=0.7)

X <- df2
Y <- df_im[18:33,]
shrink <- rcc(X, Y, ncomp = 3, method = "shrinkage")
plot(shrink, scree.type = "barplot")

grid1 <- seq(0.05, 0.2, length = 5) 
grid2 <- seq(0.05, 0.2, length = 5)

cv <- tune.rcc(X, Y, grid1 = grid1, grid2 = grid2, validation = "loo")

test.rcc <- rcc(X,Y, ncomp = 6,  lambda1 = cv$opt.lambda1, 
              lambda2 = cv$opt.lambda2)

plotVar(test.rcc, comp = 3:4, cutoff = 0.6, var.names = c(TRUE, TRUE),
        cex = c(2, 2), title = 'Nutrimouse, rCCA comp 3 - 4')

plotVar(test.rcc, comp = 4:5, cutoff = 0.5, var.names = c(TRUE, TRUE),
        cex = c(2, 2), title = 'Nutrimouse, rCCA comp 4 - 5')